Easiest choice in ages: Time and the Rani. Also an easy choice for Least Favourite Story full stop (no, let's be fair. Silver Nemesis runs it close...)
I like "Silver Nemesis." Sylvester McCoy had some real dogs during his tenure but "Silver Nemesis" hangs together fairly well. It's not great but it's a decent outing. (And I suspect it would be far better regarded had it not come out so close to the very similar & much better "Remembrance of the Daleks.")
As for my least favorite regeneration story, it's hard for me to pick. The 1996 movie is pretty terrible, despite the fact that Paul McGann is wonderful in it. IIRC, "Time & the Rani" was pretty lame but I only ever saw it once. There are some good bits to "The End of Time" but it's just so overblown that I still might pick it.