1) Why is it that people say to evolve a peculiar type of Homunculus to S? Like "Go Filir -> Sera"? Is it to combine both Homunculus Skills and stats? Do this mean that the Homun S keeps the previous skills it had before as a regular Homun?
Another question: Am I stuck with a homun after I choose it? Can I choose a leveling one before transcending and after that choosing my "definitive" one?
1. Yes, homun keeps all stats and skills. Stats only matter if you combine base type and S homun that both have bad growth in a certain stat; homun stats are capped at 150, and will generally hit that cap well before 150.
Most people argue that Amistr is the best endgame homun base type, because it is the only one that has skills that help the owner (instead of just helping homun kill - homun killing is only good for leveling the homun; once that's done, those leveling skills are not very useful) - and he's got two of them.
You can always delete your homunculus, but after deleting it, you start from scratch - you use another embryo to get another level 1 unevolved homun with awkward loyalty, and go through the whole process over again. Most people try to avoid doing this if possible. The loyaling just takes too long to remake homuns.