Some characters are better off as background characters.
But again, that's not a reason. There should always be deductive reasoning as to why one should not include the character as well as why one should include one.
I'll use Ein for example. Personally I think Ein should stay, but if there was a reason why he doesn't come back or does not return as launch build then it's because of this:
1) Ein no longer exist. As long as Hayate is here, then Ein is the shadow he left a long time ago
2) Ein was cool, but his gameplay portions weren't the best of attractions that make people want to pick him up due to gameplay reasons alone. Not many Japan players would like to use him either.
3) If Ein ever does return, he likely only returned out of pure fanservice for the teens that are horny for him, or perhaps simply out of nostalgia or pity of Ein and it's players. Me on the other hand? I'd like him to stay because there may be hope for him to retain his cool factors back but this is pure off world ideas so if he doesn't return then there are reasons for that.
You come up with possible reasons as to why a character does not return or can't be an entry. As for Donovan, he is a scientist. Scientists come up with theories and hypothesis, scientists also have a knack on experimenting on themselves to achieve a certain goal(s) of performing risks even if it messes up their body (mostly evil scientists). Donovan looks like the guy who must achieve absolute results, so a plot like this wouldn't be a surprise turn since many other games/shows etc. have characters that do this. Are they going to take this route? it's a little on the 50/50 considering Donovan has henchmen to do his work, but eventually there will come a point where the heroes will just eat up all his resources and he'll have to make his last stand before dropping for good and then a new villain arises to take the mantle. It's how things work (for the most part).