I do notice that at higher AIP levels/longer games, the special forces can get out of hand rather quickly. I've also seen some odd behavior with carriers and special forces, I've tried on a number of occasions to pop special forces carriers to kill the ships inside... only to have the carriers reform right before my very eyes. This is on the more extreme end of total ships, but it was an interesting experience nonetheless.
I think the planet had a number of normal reinforcements and carriers as well as special forces carriers, and I'm not sure entirely how they all interacted, but it was quite weird. Apparently the game wanted me to kill those 3000 ships on the other side of the planet rather than pop open the carriers and kill the ships on this side. I also think special forces don't exhibit normal carrier behavior in that they do not combine into fewer more powerful ships when burst open, so breaking open 3 carriers of SF with 3k other ships on the planet ends up putting the SF ships just back into the carrier, even if you have ships about to shoot at them.
Carrier quirks aside, special forces aren't too hard to handle generally. If they aren't there and you know they are going to show up, you can set up a beachhead and face them down without too much trouble. Trying to take a world where special forces are entrenched (along with standard threat and the normal defense reinforcements) can be hairy.
I'm not so sure they need to be changed persay, but it does create some odd dynamics sometimes. I guess you can only really be 'stonewalled' by special forces now, and only if they are reinforcing faster somehow than you are. This situation, I think, may only arise when trying to deal with the special forces on an AI homeworld proper. I've encountered it once or twice, and can be a bit of a nightmare in addition to the strategic reserve and any other local nasties, requiring grindy attrition warfare (or a few well-placed warheads if you can somehow sneak them in and get them to hit a large portion of the fleet). I suppose a nuke would also fix the problem, if you were ending the game shortly.
I think the main complaint I have about special forces is in options for dealing with them. You can try to delay the inevitable confrontation by either:
1) Diversion - Lure the special forces somewhere with a distracting fleet and strike elsewhere. This gives you a short window to do what you need to do. If that is something quick, then this is a viable option.
2) Pop command center - Obvious minuses are AI progress cost (although in some cases, like CSG, you don't' have a choice anyway). This is obviously not visitable on the core worlds and not easy to do on the AI homeworld. This only delays the inevitable though since you will have to fight them eventually at a core or homeworld.
Both of those though, only delay the inevitable. Eventually you will have to confront the special forces and that leaves you really with only two options:
A) Warheads - Lightning, EMP, nuke. all +AI progress, but saves a lot of time and will temporarily solve the problem, giving you a window large to do what needs to be done.
B) Attrition - costs all kinds of resources (metal, crystal time), but will temporarily solve the problem, giving you a large window to do what needs to be done.
Actually, now that I think about it carefully, there is actually a third strategic option where you may not have to kill the special forces. If you can somehow lure the special forces into a planet, and then seal that planet off by claiming the planets around it, the special forces garrison will be trapped, and will not attack. I've managed to do this by accident every now and then (although usually to my determent, on top of the travel lanes I wanted to use.) Having the 'perfect area' to lure and seal a large chunk of the special forces away in would require some great foresight, planning and a bit of luck.
Barring that very specific case, you still eventually will have to confront them, and that means back to one of the two combat options: warheads or attrition. By itself, this would be a problem, but special forces don't exist in a bubble, they exist in the large context of the overall game, and add that direct confrontation element that you either have to accept or strive to avoid while constructing and executing your larger strategic plan.
The only real way I see the current AI special forces behavior becoming a problem is if all AI homeworld battles toward the end game end up a giant slugfest between the human fleet and AI strategic reserve + AI special forces, and I don't believe that is necessarily the case right now.
I did try sniping the AI homeworld cmd station once through it's shields without combating the core reserve and/or special forces, without much luck (I couldn't provide enough cover to the ships that could shield-penetrate). I'll have to try again one day, but every game I've played has required a moderate slug-fest with the homeworld strat reserve, but it's usually not terrible since the strategic reserve doesn't reinforce that fast, you have plenty of time to act after destroying it.
I guess it if it causes the taking of other strategically important assets to slow to a grind every single time, that would be another problem, but I don't think they reinforce quite THAT fast.
Edit: Observations are on difficulty 7. I'm interested in finding out what the special forces reinforce rate is vs. player potential refleet rate, and how they compare, to see at what point you can no longer win due to the special forces and player fleet killing each other totally, and the SF fleet reinforcing faster.