I can't say I'm terribly surprised that it's restrictive and makes it difficult to do such things. It isn't a terribly common thing to be able to easily add/remove things like character classes unless it was designed from the ground up for such things.
Personally, I'm mostly fine with the Basic Types being what they are, as it allows them to act as a means of learning how the different aspects of the gameplay work before diving into something challenging like the Forte-types and the Hybrids, much less the Master types. Any kind of notable change to them would require a notable rebalance to all of the types, as then you start to skew the roles that each of the Expert types were meant to fill.
Unless you're planning on expanding the roles of the existing Master-types so that instead of being hyper focused into a narrow area of specialization they're the supreme masters of all things Striking, Ranged, or TECHNIC respectively. Although that more or less works for the Fighmaster and Gunmaster to allow them to use all of the weapons associated with their specialty (though the Fighmaster would need some kind of limited Ranged ability, to pair with the 1-handed Striking weapons, and the Gunmaster would need mirror treatment) doing that for the Masterforce starts to make the Acrotranser quasi-meaningless as a Masterforce could be just as good of a Support Member, while also being the supreme nuker. I'd personally only consider it worth seriously trying to do if the Masterforce could also be given all of the Limit Break bonuses to TECHNICs, allowing them to still be more useful with offense than support, and do a minor rebalance to the Acrotranser to be more 'Red Mage' like in that they are a Jack of All Trades, Master of None and can do everything to a nice extent but at least one other type is still better. The limit of only 36 Photon Arts at a time on a character would help in that regard (actually, it isn't even possible to have all of the TECHNICs, both Attack and Support, learned at the same time because of that limitation, and with a max of 24 slots amongst the active weapons of your weapons palette it is a bit questionable to change that anyhow, though being able to increase the limit to enough to learn all TECHNICs at once would be nice, in the Episode 1 content (Ethan Waber's story) it was possible, then they added more TECHNICs, but I think the original count was right at 36 TECHNICs).
I'm sure if I put some time into it I could come up with a way of rebalancing all of the types so that the Basic Types could be expanded some in functionality. Of course, this would require them to be able to have their Max Type Level increased from 10 to at least 20, possibly 100, so that they can match out against the Expert and Master types, but then you'd have to increase the requirements for both the Expert types and the Master types, and then they'll also be treading on the roles of the Forte-types. Then again, restrict them to a Max Type Level of 20, but increase the max rank of the weapons they can currently use by one tier (so B-Rank to A-Rank and C-Rank to B-Rank) along with allowing them some additional weapons at C-Rank. Then you'd probably need to increase their Photon Arts limits, though I'd only do their primary PA's by one tier, so 30 instead of 20, and leave the others alone. Actually, make it so that only the primary weapon types (Striking for Hunter, Ranged for Ranger, and TECHNIC for Force) get the rank increase as well, and you'd be able to limit how severely they'd trample on the existing Expert Types, then you could still allow them a Max Type Level of 100. Also, I'd keep the Force with no Limit Breaks so that those bonuses would be a special part of using an Expert or Master type with Attack TECHNICs. Maybe re-work the Guntecher a bit so that they are less capable with Striking weapons to make them more focused on Ranged or TECHNICs, better favoring them being a Ranged Support type. This would then work in with the rebalance of the Acrotranser I mentioned above. We'd probably also have to re-do the Fighgunner and Wartecher some to get them more focused towards their roles, namely a Striker with some Ranged Ability and a Techer with some Striking Ability respectively. Then we'd need to tweak the Acrofighter to be more balanced between the Striking and Ranged aspects, since we'd essentially be removing that balance aspect from existing Expert types. We'd also have to readjust the ability balance of the Forte-types as well since they'd now become more of a glimpse into the re-done Master types.
Then again, the Acrofighter is the expert in the use of the 1-handed weapons, so if we just expand that to also include the twin weapons (which they already have most of as A-Rank weapons, so bump them up to S-Rank and add in the two, I think it was, they don't have as at least A-Rank) and then drop some of the 1-handed and twin weapons on other types that have them at S-Rank down to A-Rank, and possibly even remove the ability for them to use one or two that they can currently only use at A-Rank (with the exception of the Forte-types, keep them with the ability to use their own focus ones that they currently have, since the Master types would be gaining the ability to use them, only makes sense, just limit them to 1-handed weapons from their non-focus area).
There that's what I've had for thoughts on what it would take for a rebalance to increase the relevance of the Hunter, Ranger, and Force, while I've been typing up a response to you. Those are just shy of direct stream of consciousness as they've happened for me. I'm not saying it couldn't be done, but I do have a small question before attempting such a thing: Is the info for the limits and abilities of the types stored server-side or client-side? If it is server-side then we could set-up a test server (which I've noticed you already have one) to use to test out a massive rebalance of the types and see what people think of it. If it's stored client-side then it would be much trickier to test that out before doing a massive Clementine-wide implementation.
Now, if I go over to the Clementine wiki and look at the existing information for all of the types it'd probably only take me a couple of hours to through together a thorough rebalance plan so that the Basic Types can be given a useful degree of viability for mid-range content (very hesitant to balance them to have any degree of viability for late-game stuff, unless we keep them severely limited outside of their focus areas, just so that we can maintain some degree of viability for the Acro-types) complete with rebalancing all of the remaining existing types. Personally, since there are S-Rank versions of every weapon type I'm perfectly fine with expanding out the Master types so that we can use all of them with 5th Form Photon Arts (that's levels 41-50) and the speed boost. It would also require some rebalancing of the weapon stats, so that there wouldn't be any weapon categories where the strongest weapon is actually an A-Rank weapon and not an S-Rank (or as I like to call them, SS-Rank for the 13-15 star weapons, as there is a 15 star for every type if I recall correctly, again I'd have to check that). Although, I do need to test to see if the Card weapons allow for First Person Aiming or not. I doubt it, since the only other Ranged weapon that is 'optimized' for groups that does is the Laser Cannon (at least, I don't think the Crossbow does, though I could be wrong), but if they do I might through in a minor tweak to the idea of the Master types being the supreme masters of their respective areas to give the Masterforce S-Rank Whips and Cards, while the Fighmaster and Gunmaster won't get them, along with the ability to use Level 50 Skills and Bullets (just for them, since they won't be able to use any other Striking or Ranged weapons) to reflect the fact that those two weapons are mostly treated as being 'for TECHNIC users' amongst the other types (even offline AoTI did that, as only the Force could use the S-Rank versions). It would also give the Masterforce an FPA weapon to replace the C-Rank Handguns that Clementine currently gives them to maintain their solo viability (as well as a Striking weapon so they don't have to burn PP just to destroy objects, allowing the Gunmaster a very limited selection of 1-handed striking weapons does that for them already). And we can't forget tweaking the ATP, and possibly ATA, multipliers of the Photon Arts for weapons that currently can't be used in 5th Form as that gets added, assuming that can be done in the first place. I'd hope so (and that was going to be one of my two questions before presenting the four additional Master types I'd come up with) as otherwise there isn't much point to giving additional weapon types to the Master types.
That's just the story of my life. I've missed out on quite a few things because of being only marginally better than living on the street for my adult life, but it was probably an effort on their part to keep people from pirating those portions of the story. After all, how many MMO's in general do you know of have the story data portions stored with the client data anyhow? That's typically all server, so it's hardly unusual they did that, especially with the need to keep the game relatively small since 10+ years ago people didn't typically have 100+ GB drives in their computer systems and such, so a single game needing 10 GB would be an issue. Mind you, I highly doubt the game would be that big with all of the story data combined (unless they had a lot of those spectacular CG FMVs just for Episode 3, if memory serves they only got added to Episode 2 with the release of AoTI), but don't forget, the Clementine Installer is just over 5 GB itself, and once installed it's sitting around 6.2 GB. That only leaves about 2.2 GB of space on a single Dual-Layer DVD for holding the game. That now starts to lean towards the gaming being force to be installed on the console to be playable (and don't forget, the PS2 HDD's were only something like 10 or 20 GB in size, that's a LOT of the HDD consumed for just the one game) depending on just how much bigger all of that story data makes it. Even on the PS2 those CG FMVs took a lot of data space, that's why the .hack games only had their respective FMVs viewable on the volume they were originally shown in, despite being able to unlock them in later volumes (though if you had the disc for the earlier volume you could view them, you just had to swap discs before and after).