I predict some abilities to be replaced, as people pointed out. It would be a great opportunity to fix past gen mistakes and prevent a retarded omaunt of ability slots. Let's make some examples:
-Dual abilities on legendaries is actually wrong, since legendaries appear once. Sure, many legendaries got pressure, so I understand they gave them a second ability, but they actually just should have replaced pressure instead. (and many legendaries didn't get a very interesting ability either, such as Articuno, Mewtwo and the Sinnoh dragons). I do want to make an exception for legendaries that have multiple ways of summoning, athough that hasn't been done yet (Would be cool if they made a R/S remake, and gave the regis two ways to summon).
-GF will likely introduce a Hail equivalent of Sand Rush (I call it Snow Rush) and Stoutland certainly deserves it. But he already has three abilities. Two of them leave him in dust, so it would be a good idea for GF to remove them on him and give Snow Rush instead. (Also, Sand Rush and Snow Rush pairs very gimmicky).
-In DP, Hitmonchan got an ability that boosts all punching moves. One would assume Hitmonlee would get an ability that boosts all kicking moves. But no, he got an ability that only boosts (Hi) Jump Kick (which was crap back then), along with an array of moves he doesn't even learn. Fix that, GF!
-Some more mons should gain a signature ability. Some funny ideas would be an ability that combines all non-signature sun-consuming abilitys for Sunflora and, an ability that priorities Electric moves for Raikou (similar ones for Entei and Suicune), and an ability that removes hazards on the end of each turn for Hitmontop. Of course, these should be their only abilities, so it would cause an ability replacement.
-I'm of an opinion that all eeveelutions should have the same ability (I was thinking of Adaptability and Quick Feet), as part of their gimmick. Not sure if GF can do this at this point, as Espeon would severely dislike it.
-Blaziken would stay in Uber if it kept Speed Boost. Starters shouldn't be uber, so I guess GF will take it away from him.
-GF blew several dream world abilities. Most notably are the Regis' abilities, as they would be perfect recepients for Analytic. (Ice Body is decent, but relies on the least used weather. Surdy is good, but kinda useless on Regirock, and Light Metal is just a shit ability in general). Other notable mons are Rapidash (it should have gotten Sap Sipper), Farfetch'd (it should have gotten Super Luck) and Ampharos (it should've gotten Lightningrod).
-GF also blew the gen3 ability distribution a little bit. I mean, almost nothing got Volt Absorb (Ampharos deserved it!).
-Ditto should have Imposter as it's only ability.
I would also like to mention something about the in-game mechanics of abilities, even though it's kinda off-topic. Up until now, every pokemon has one or two ingame abilities with the same frequence of appearing anywhere, along with one hidden ability that has to be obtained by event. I find that actually very stupid. In my book, every pokemon should have up to three ingame abilities, and the frequence of each ability varies per ingame location. That said, some ingame locations feature species with only it's first ability. Some abilities will be version exclusive, some will be event exclusive, but the amount of that will be limited. Some other factors can play as well, such as season, day of the week, and day/night.