I'll take this in turn:
1) Opinion, I suppose. I'll agree I wasn't a huge fan of Bowser Jr. getting in, but I thought the additions of Shulk, Duck Hunt (who I initially despised and eventually turned out to really enjoy), Mega Man, Villager, and Robin/Lucina definitely made up for it.
2) Let me address this first by saying that one character from each franchise was simply a "clone" character, meaning not as much development time had to be spent on them. The reason Lucina/Dark Pit were chosen was because their moveset would be fairly easy to replicate. It's not as if their spot in the game was given to them over an entirely new character with a new moveset; they're essentially a bonus.
Secondly, I quite like FE, so shup you.
In all seriousness Uprising and Awakening were fairly recent titles and so the characters being in that game likely owe their appearance to that. I do think you're dismissing the popularity of the two games, though; they both sold pretty well for 3DS titles not named Mario, Zelda, or Animal Crosssing.
3) Define "innovation," because there's quite a bit new to Smash 4; 8 player Smash, an actually functioning online system (which you may or may not even consider innovation), overhauled classic mode and event mode, whatever smash tour is worth, etc. If you simply mean from the actual gameplay in battles itself, I'd still argue there's a fair amount of innovation to be had there, at least for a fighting game on it's fourth installment. But the ledge mechanic was overhauled, perfect pivoting is now a thing where it wasn't in Brawl (at least to my knowledge), and many of the characters themselves have undergone significant changes. Perhaps more to the point, though, a fighting game in its fourth installment probably isn't looking to make many "drastic" changes; it's rather simply looking to fine tune what it's doing already. You can argue as to whether it's doing a good job of it, but at this point Smash is less about major innovation and more about trying to get down what it's already doing.
4) I'll agree with this
5) I have no idea where you got the notion that Earthbound is far more popular than Fire Emblem, but whatever. I do wish Ice Climbers had been left in, but that was due to not wanting to jiff the 3DS version (a rather stupid reason imo). Calling Wolf a completely original character is nothing short of hilarious, however.
In short, some characters got left out; but just in terms of a franchises' popularity now, the cuts certainly make since. Uprising was a few years ago, Awakening was less than two years ago, the last Star Fox game was in the DS era, and the last Earthbound game was before the 21st century.
6) I didn't like it much either, but so what? It's a totally optional feature, and only happens on one stage and only if you taunt repeatedly for it
7) I guess? Trophies are bad? I feel like this is akin to complaining about the title screen not looking spiffy enough or something.
8) Stickers were cut to make room for custom moves, and the character stats are far more balanced than stickers. You can actually use them in play without simply breaking a character
9) I'm actually pretty certain the Wii U has more; Wii U has 46 (47 whenever Miiverse comes out), and Brawl has 41. Some stages are meh, I'll agree, but I think some are quite well done. Opinion's opinion, I suppose.
10) Subspace was garbage; replacing it with actually focusing on balancing the roster and making the online worth half of a chocolate biscuit was a much better decision.
