I assume you are referring to Psionic Scream, which in no way prevents Titans from using their abilities (though it still does damage to them)...

Reverie, detonate AM, ion bolt, magnetize, and phase out hull do not affect Titans either...

The only cap abilities that affect Titans' ability usage are EMP (removes AM, but still allows abilities to be used), Disruptive strikes (performs interrupt and increases ability cooldown), and the new Discordia's ability lethargy (increases ability cooldown)...

Each faction has one cap ability that directly impacts titan ability usage, and none of them do a particularly great job (multiple Dunov's with EMP is the only exception)...

Capital ship abilities should be able to work on titans.  They should have some performance degradation, say ion bolt level 4 would have a 60% chance of shutting down a titan.  Also, the efficacy of this ability could be reduced as well, say the duration of the "stun" would be cut in half, or cut in 1/3

It would not be totally reliable, yet it still would have a chance to work.

All capital abilities could be balanced against titans this way, instead of having them do pretty much nothing against them as it currently is in the game.   This is a poor design decision because it limits ability use in the game, which would limit a players fun factor as well. Also, many of the capital ship abilities would allow for many more creative ways to use/counter titans, so that titans aren't the "single path to victory" in a large multiplayer game. 

Balance could be achieved in that low level capital ship abilities have a poor chance to work on titans(low % chance, indicated on the tooltip), while high level versions (Ability level 4) would have a good chance to work on titans.  This would allow for capital ship specialization to play a larger role in the game then it does currently, as your capital will specialize in assaulting a certain titan to assist your fleet.  This would increase the fun factor quite a bit as well. 

At first I was in favor such changes, but I've come to think otherwise...you can only have 1 Titan, but you can have 14 other capital ships...even 5-6 capital ships is enough room to allow 2 or 3 of the same type that just spam some ability to prevent titans from using their's...

I mean seriously, imagine if Detonate AM affected titans...2 radiances spamming that and any titan is pretty much negated entirely....being able to use ion bolt on titans would be even worse, two akkans in their own culture would keep it shut down long enough to decide most battles and pick off the titan at the end...

Tacking on a "chance to affect" I don't think is going to help...the biggest problem I see is that it just adds more blind luck to the game and that is not going to go over well...chance to affect abilities are better left for AoE debuffs or for frigate abilities that are not very powerful and are always going to be used en masse...

Besides, a percent chance just raises the threshold...if detonate AM has a 50% chance to work, then instead of 2 radiances now you need 4 (and actually, 3 radiances would be enough unless you ran into some really bad luck)...

I think its balanced as is. The Star Bases were designed to protect a system and the Titans were created on their scale and to counter them. If you let Titans be effected then star bases should be too.  That would through the whole balance out the window since entrenchment.

I suppose if that chance was like 1%, up-gradable to 3% with research then maybe.  It would be a wild shot, golden bee-bee sort of thing. Proton torpedo down the exhaust tube sort of attack.  As an act of desperation. At that low probability most wouldn't want to waste the antimatter unless they felt they had no choice.

50% is just a ballpark number...i'm sure it would be balanced to be far lower, for more capital ships.  If it was a 5% chance at ability level one, then it increased by increments of 5% per ability level then you would get a 20% chance max to influence a titan.  So with 5 capital ships of the same time the titan could be effectively limited in what it could do.  To be fair, the game already has this counter in it, 5 dunovs will not only render a titan helpless, it will do so while doing significant shield damage.

This changes tactical risk assessment.  Or in other words, the titan warps into a situation and the player knows the risks, yet the player can still choose to do so because they can overcome the potential hazards, based upon what they know.  this can turn against them.  Certainty in combat is a false dream, its all about adaptation at a moments notice. 

This idea only adds finesse to the decision making in the game, and makes predictability in some cases a crapshoot.  Yet the overall strategy would be little impacted by this.  This is not nearly the game changer that you think it is, chance abilities can be quite effective.  Its a well documented fact that random chance is quite fun indeed.  I recall world of warcraft using this quite heavily in their more recent class abilities, and to a very great improvement to the game I might add.  The critical hit in wow also was a huge seller, a random chance ability that you had control over that blasted big numbers onto the screen. 

I see your point about the quantity of capital ships...

Yet, remember, titans have incredible fleet destruction capabilities.  It takes a moment for your rebel titan to blast your fleet to kingdom come.  It takes a few more moments for most of the other titans we've seen to blast the fleet to kingdom come.  Tec titans will last a while vs any opponent, they are tanks!

I would say as a general rule disruption abilities should have a far lower % chance of success, perhaps you have a 10%-20 chance total at ability level 4...in this way multiple akkans would have only a chance to disrupt.  Any fleet that focuses on too many capital ships will be firepower starved anyways, its always been a really big balance of fleet capability vs fleet firepower.  TEC Titans are great in that they don't really sacrifice fleet firepower at all, in fact they ADD heavily to fleet firepower.

The point being, a few capital ships could deter a titan if they are of the proper configuration.  Adding different ways a titan could be countered won't negate their influence in the game, they will ALWAYS be effective at what they do.  Ships that limit them will become targets of priority, and depending upon the strategy these priority targets will change. 
As it stands for the TEC, the dunov is public enemy number 1 and will be recieving the brunt of my fleets firepower.  this will get old after a while.

3% chance in a game mechanic is is VERY bad idea unless the mechanic is either very fast repeating (like critical hit chance with fast attack rate) or it affects many targets at once.

Would you really want the titan fights to boil down to one player getting lucky roll of a dice?

I personally think that the disable/debuff abilities should work on titans, but oly with limited effectivity (like 50%). I think it should be possible to lock out a titan, but it must not be easy (if you needed 5 capitals casting correct abilities at correct times, it is fine with me, because it means that the titan effectively locked out 5 capitals + a lot of the player's attention has to be focused on maintaining the lock).