I did an ability run-through
before, and so I'll do it again. I'll start with abilities that others have mentioned that I outright don't like, but I won't mention abilities I bashed last time.
Inner Focus: This is supposed to help beat Jirachi, but as Deck Knight calculated, it doesn't do enough. no
Marvel Scale: The boost from getting poisoned seems like an interesting idea, but ultimately it just doesn't seem to fit. Your Def is boosted... but you're poisoned -.- Not to mention CAP 11 has Taunt as a Type-Move requirement. no
Sticky Hold: Togekiss honestly doesn't come across as a Trick magnet to me. Because of this, the argument for this is rather weak. no
Static: Yet another example of people not knowing how an ability works. None of what CAP 11 wants to switch into is a contact move. This amounts to a possible "screw you" to enemies wanting to Close Combat CAP 11 for the KO. I just don't like hax abilities... no
Steadfast: Same reasons Deck Knight stated, mainly it is simply unreliable. no
Unburden: The possibility of CAP 11 going it alone seems interesting, but I feel that CAP 11 is already good enough as a standalone and Togekiss really ought to be an improvement to it. no
I'd like to discuss stat-altering abilities as a whole because they're something that I almost outright rejected before Rising_Dusk convinced me to reconsider Motor Drive and then abandoned the idea. I'd like to say right now that I do not want the second ability to outclass Volt Absorb significantly, and due to the evidence thrown around last time, I'm rejecting Motor Drive under this conviction. However, the ability must also be a convincing alternative to Volt Absorb. (More on flavor abilities later.)
The abilities suggested so far that attempt to alter stats, or have a roughly equivalent effect, are Download, Hustle and No Guard (which I considered supporting last time). I'd first like to address the physical boosters. Consider that CAP 11's Close Combat can already be made almost as powerful as Scizor's Technician Bullet Punch. Consider also that CAP 11 is nearly guaranteed to have Bulk Up and Taunt as Type-Move requirements. Hustle and physical Download have the potential to be overpowered. If I were to choose one of the two, I'd go with Download because of the lack of a luck factor. However, one should also consider a "weaker" ability like Adaptability to boost CAP 11's STABs instead. Special boosters are in a similar predicament. Special Download may prove to be overpowered if we're not careful. Interestingly, if we consider Aura Sphere vs Focus Blast, Adaptability and No Guard provide the same special offensive boost, though Adaptability also boost physical STAB and doesn't do anything to opponents' accuracy. I'd like to stress the "overpowered" worry for both spectra because we did set base stat limits and these abilities basically attempt to break past them.
Lastly, I'd like to address two abilities meant to patch up type and status weaknesses. Thick Fat is an ability that I ultimately rejected last time because it didn't seem all that helpful compared to Volt Absorb, but it seems to me like a decent alternative ability because of Starmie and bulky Waters in particular (though I'd imagine that CAP 11 would still have trouble with bulky Waters). The other ability is one that I supported last time, Immunity, which also seems to me like a good alternative ability if the team builder is worried more about defensive threats throwing Toxic around.
So at this moment, the abilities that I believe are far and away the most appropriate for the alternative ability are
Adaptability,
Thick Fat and
Immunity.
P.S. To the people suggesting flavor abilities: I believe that you should merely push for a No Secondary Ability while putting forward the possibility of a flavor ability. This kind of thing ought to be decided after the concept art is chosen.