I make an example, take Mewtwo:
It has its onw page, in which you write, as you did, "Mewtwo can Mega evolve via Mega Stone in MegaMewtwo" (with the name "MegaMewtwo" as an iperlink leading to its own page - as it is for normal evolutions), you put in the page all the conditions it needs to Mega Evolve (or change forme, if you take, for example, Deoxys) and then you continue to talk about normal Mewtwo, mentioning, when you need it, its Mega Evolution, keeping, in this way, the information still higly accessible. The you could create a chart in which its Mega Evolution/Forme Change is shown (just like normal evolution!), with links leading to the Mega Evolved/Forme Changed Pokémon.
It won't be difficult to find them - is difficult to find Forretress page in the Pineco one? I don't think so. Then I don't think this would bury information under sub-pages, but it would add more interesting and specific stuff to the encyclopedia.