Bad decisions
Huge starting roster (I don't get why they gave us 35 and even more in the Wii U version. It's like they think fans hate unlocking things.
The unlocking of custom moves
Irony of that aside
I personally do hate unlocking things. Even to this day it's a headache for tournaments because the extra settings menu isn't available or the full roster someone hasn't been unlocked. Melee at least allows save file copying, and years ago people found a way to break the save transfer block on Brawl, so as long as 1 person had the foresight to load a cracked save on an SD card...
Now it's harder to do that on Smash 4. To do this for players on 3DS, someone needs to have an Action Replay, a computer, and an internet connection to update their cartridge to have all the unlocks available to them. Day 1 Wii U tournaments probably won't even have the stock time limit available to them if it still takes 10 hours of play to get that feature like 3DS did.
As you said though, unlocking Custom Moves just plane sucks. Even more so because some characters go from being kind of 'meh' to actually being threatening. For example:
Pikachu getting a Zero Suit style stun on Neutral-B from Thunder Wave
Charizard's gains a terrifying amount of mobility and edge guard power from Dragon Rush
Ganon can actually punish many projectile spammers instead of being eaten alive by them with the warlock kick that pops in the air first
Now if they were say... unlocked through a shop you spent your smash coins on and could actually pick the ones you wanted, that would be amazing. You could actually unlock everything by doing nothing but multiplayer!
Instead, the team apparently thought that players would want to grind single player for 100+ hours to get the custom unlocks. And salt in the wound is them tying it to custom equipment. So you can't even use random if you have customs turned on, because the random choice will also get crap like 'Auto-Healer' or stupid high defense which makes KO'ing go from reasonable to "WHY ARE YOU NOT DEAD YET?"
Seriously, if you have a tournament scene that wants to use customs, someone should invest in an action replay to unlock all the customs for the group. If you're playing on Wii U, I think only 1 person would need a 3DS with everything unlocked to transfer the custom build to the Wii U. I don't think it will actually unlock that custom Wii U side, but you can at least still use your set.