Because it seems to be a hot topic. I'll start off just listing a few things I've been able to check.
|Base Card||Base Ability||Booster Card||Booster Ability||Ability Lvl Chance|
|U Rare||3||U Rare||1||7.5%|
|U Rare||1||U Rare||1||15%|
|SS Rare||4||U Rare||1||8%|
|SS Rare||3||U Rare||1||10%|
|SS Rare||2||U Rare||1||13.4%|
|SS Rare||1||U Rare||1||20%|
Quick thing I noticed is that I tried using the same Ultimate Fist Iron Fist Rare on both a base SS Rare Captain America, which yielded 6% and on an SSR+ Nova, which still yielded 6%. So, at least for the moment it would seem that matching alignments has no bearing on ability boost chances, nor does fusion state of the base.
Also of note: Using UR+ Professor X with maxed level or UR+ Mr. Fantastic which was level 1 did not effect the boost chance at all, so apparently the base card level also makes no difference as far as I can tell thus far.
Next notation: using SSR+ Nova as base and boosting with Rare+ Nova gave basic rare boost probability. Fusion irrelevant entirely it seems as far as boosting ability chances.
Obviously heavily a work in progress, I just wanted to get something quick down while it was in my head. I'm thinking I'll stop with SSR cards as the base, because I figure most people aren't going to care about the ability boost chance on anything lower right? And since the ability level of both cards obviously effects probability, then the chart is going to get a little long possibly, so I need to save space.