I don't know about the changes of abilities. You really have to be careful,since an ability can make or break a Pokemon.
If you do decide on changing them, try to even things out between the three starters, or the "balance of power" might be all messed up...
Example: Magma Armor on Meltell would be somewhat pointless, considering that it will turn out to be a Fire/Rock type, you almost never would use a Ice type attack against it. And even if you did, the chances of being frozen are rather slim.
Vital Spirit on the other hand is extremely useful. If Squibeel is to be a Sweeper, it will benefit greatly from its sleep-immunity. That's because one of the few ways to shut down a sweeping attempt, is to put your opponent to sleep.
As for Water Veil, its not bad, but not good either. It mostly depends on what Freezpools role will be later on. Lets say it'll be a Special sweeper, then Water Veil would be almost useless, since it cuts Freezspool Attack stat, but it is its Special Attack, which it would rely on.
If it where to be wall(physical or special doesn't matter), Water Veil would be more helpfull, effectivly shutting down Will-o-Wisp.
On a Physical Set, it would gain the most from its ability, since it would be save from the Attack reducing effect of a burn condition.
So you see, abilties are really important, and you should be very careful when making changes to the starter's abilities.
If you really change them, try picking beneficial ones, that will support the pokemon in what their role in a team would most likely be:
Squibeel- Vital Spirit / Limber /Guts
Meltell- Shed Skin / Shield Dust / Marvel Scale
Freezpool- Water Veil / Water Absorb/ Swift Swim
Now for the explenation:
Squibeel in my opinion will be a classical sweeper, be it spacial, physical or mixed doesn't matter for the first two option. They'll both be helpful, as they effectively shut down one of the two most hated effects for Sweepers: Sleep and Paralysis. The Third Option would only benefit a Physically inclined set. For a specially focused set, you might want to go with Clorophyll.
Meltell has abbilties that help it fulfill its tanking/walling options. Shed Skin will heal status effects like poison,sleep or paralysis, that might get in the way. Shield dust prevents added effects from happening, most notably flinching and poisoning from poison type moves. Marvel scale will boost its defense even more when afflicted with a special condition, which on a walling set is very helpful.
I don't really know what Freezpool will turn out to be, sweeper,tank,support, but either way one of those abilities will prove helpful. I already talked about water veil before, so that should be clear.
Water absorb is great for switching in. I would have prefered Dry skin, but that's a D/P ability, so that wasn't an option. But Water absorb should do just fine. Especially if you are good at predicting.
Swift Swim would be most helpful on an offensive moveset. I don't know if Freezpool will be a fast pokemon, but if its speed stat is anywhere from poor to average this will definately help him out. Set up a rain dance, and start sweeping. Especially since it boost Water type moves. Imaging A STAB Surf, that gains even more Power thanks to raindance ;-)
So sorry for the long post, I'll try to shut up earlier next time, just wanted to point out how important abilties are, and that they should be handled with care ^^
And as always, this is just me. xD