The problem with evolution stones is that it opens a whole can of worms handling evolution. Taking Eevee for example, many of its Eeveelutions don't use stones but other means, such as Espeon when leveled up both with a high friendship statistic and during the day or morning. Both concepts way outside the scope of RMRKMon.
As for custom pokemon, the question of what IDs to use for them would crop up. Eventually over time we'll add newer gens of pokemon, and Nintendo will I assume continue to release games. Giving them IDs way higher than any likely pokemon would break a load of functions that expect consistent IDs (lists, RNGs). This is technically why missingno. exists in RMRKMon, just to offset from the default array key of 0
I have thought about evolution before, but by another means. Being online for extended periods of time or making posts gives you EXP points, which you can then spend on evolving a pokemon. For each pokemon, I'd store an "evolves from" field and then you could go to a page to spend your EXP - if any pokemon evolve from any of yours.