I'm playing through Pokemon Conquest at the moment and I noticed that it is still called 'Parlyz Heal' in that game too, even though they had the freedom to use however many letters they like on everything. If they didn't call it 'Paralyze Heal' in Conquest then I really doubt they are going to retcon the names of anything in any game. Nor should they. It's name is Feraligatr, not Ferilgator, regardless of why.
The easy way to find out if it'll get an extra vowel is to hunt down the name in other forms of media that don't share the character limitation that existed prior to this. If things like the anime and manga have the names as Feraligatr and Victreebel, then I highly doubt they're going to change the name.
As for whether I think they should or not, no, I don't think they should add the "missing" letters. Even if their names became as such because of the limitations, pokemon names don't have to strictly follow the words they're based on. They don't need the O in gator to make Feraligatr's name. The inspiration may be there, but it's just that. Inspiration. Not an exact spelling. Seel doesn't have an A where the second E is. Lickitung isn't Lickitongue. Scizor isn't Scissor. These are just examples, but they're meant to show that pokemon names aren't meant to be strictly exact spellings.
That, and when I see the O added to Feraligatr or the L added to Victreebel, I can't help but cringe purely on reflex alone. It looks so wrong to me.
Can I also point out, I see where people are getting Feraligator from, even though I dont agree with it, but where does Victreebell come from? And dont say Weepinbell. They may be in the same evolutionary line, but they are still different pokemon. There is absolutely nothing wrong with Victreebel. It's pronounced the same, and looks better as a word.
I kind of see this issue similar to how many Pokemon in First and 2nd gen were coloured with 1 or 2 colours due to limitation of the gameboy, and then when 3rd gen came out, those same pokemon could now have 3 or 4 colours because the GBA advanced enough. Likewise, now that our 3DS can handle 12 letter names (is this confirmed?), Pokemon that were meant to have 12 letter names should get updated.
The difference here is, they still had official art that was accurate(They haven't ever actually spelled it Feraligator anywhere, have they?), and the first pokemon games were in black and white anyway. A graphical update and a name change are two different things.