This is a really interesting topic that might actually yield some fruitful debate.
On the one hand, I'm a firm believer that GameFreak cares very little about balance outside of some stereotypical powerhouses and the new Pokemon they're bringing in. They never do anything substantial with older Pokemon if they're not throwing them a Mega, and that's mostly to prevent breaking backwards compatibility. To that end, I can't fault a hacker for wanting to make changes to a Pokemon's movesets, valid abilities, or base stats. That is, as long as the changes are not absolutely absurd or completely unbalanced. For a great example of rebalancing done right, check out
Yet Another Firered Hack by DoesntKnowHowToPlay. It's stock Firered plot with balancing that is near perfect, and a great example to learn from.
However, I myself am very hesitant to change those things in my own hack. I'll often pull from existing movepools from all of the generations when deciding if a Pokemon needs an adjustment, not giving them a move if they've never
ever had access to it. But if that Pokemon had an obscure, one-time event back in Gen 1 that granted it a move, I'd certainly consider handing it out if it's needed. As a rule, I never touch base stats. I'm a bit split on abilities. On the one hand, we don't have perfect implementation of all of the current abilities yet. On the other, many Pokemon are functionally
completely different Pokemon without some of their current abilities. Fortunately, I'm not really in a position that I'll have to consider that yet for many Pokemon, and when I do it'll be negligible. Most of my hangups with changing things like this come from a lack of confidence in balancing things on my own, and a general desire to maintain trade compatibility with the stock Gen 3 games for my hack. I figure that
official GameFreak imbalance is better than imbalance that I myself am forcing on my future players.