Lol

I like your ideas, cut the Thor in half!
Or make it a mobile super bunker!
Anyways... I just have one idea right now, I'll be posting the other four as they come to my mind.
For
Battlecruiser.
Yamato gunner
Missile Pods launcher.
Defensive Matrix holder.
Well, if it's going to be the way it's described there... I'm afraid I don't like some details. i.e. What's that "Specialization" ugly crap? Why not just only require the research to have the 3 abilities available for all BC?
So, the stats would be
Yamato Gun Cannon, Missile Pods and Defensive Matrix are available after the respective upgrade is done at the Tech Lab or whichever building they had to be done.
However, once any of these is used (i.e I cast Yamato Gun Cannon) the whole system enters in cool down for a reasonable amount of time let's say 35 seconds.
This means that said Battlecruiser won't be able to cast any ability for that time. If you consider that, in original SC a battlecruiser won't be able to fire again for a very long time, (the time it takes to recharge enough energy up to 150) and considering the best case:
a Battlecruiser with full energy that has the Colossal Reactor upgrade has 250 energy, so after casting Yamato Gun it will have 100 energy, which is enough to activate it's defensive matrix, however since the whole system is in cooldown, it will have to wait 35 seconds to use it.
I think this is a lot better than having different types of Battlecruisers and depriving the ones that have the defensive matrix to use the yamato cannon and so on.
-550 Hp instead of 600, after all now all BC's will have the defensive matrix.
About each ability:
-Yamato Cannon
Only change this detail: since it's a massive beam of concentrated energy, make it deal splash damage in a very small area ONLY if it was cast to ground units, so if it's a very tightly pack of units, the one that received the blast would take the whole damage, the other ones in a very small radius would take 30%.
It won't deal splash damage when cast against air units.
-Missile Pods
If i'm not wrong this is an anti-air attack that damages an area, right?
if that's the case, then it's OK.
-Defensive Matrix
Ok, Science vessel's def. matrix but in the BC and can be self cast to vary...
sounds cool, but let's tweak it a little, how about instead of just absorbing 200 damage, make it 150 but, the shield itself takes 15% reduced damage from large armies, (which is in fact the opposite mechanic to the Inmortal's hardened shields)