This ruleset reads like a rough draft. It has a lot of general direction things right but botches the particulars pretty badly and ends up not being a very good ruleset if used as it stands.
Let's start with stages. 3 starters is just terrible; the stage list is small enough every legal stage could be a starter, and it has baffling exclusions like Skyloft and Wuhu Island that are just obviously okay stages. So few starters skews match-ups; a lot of match-ups get more lopsided when one side can force either FD or SV (the two flattest, least dynamic stages in the game), and since in most MUs one side will really not want FD and the other will really not want BF this kind of small starter list is just forcing SV every game which is a really unfair bias toward characters and players who particularly like SV and is also going to just plain make things boring for stream viewers and a lot of players. It just doesn't make sense to ban Skyloft and Wuhu; there's just nothing at all wrong with those two stages, and they're pretty much of the exact same character as all of the other stages they have legal so those two don't really push any boundaries versus what they already are accepting in terms of quality stages.
The custom thing... It wasn't surprising to me but the way the Miis were handled does give some hope. The Mii situation makes it overwhelmingly clear that customs in themselves are not the problem (like the mere idea of having multiple movesets). They're citing unlocking issues which would have made sense a month ago... but 3ds transfer pre-event via the system we've all been working on as a community solves this problem. It's especially easy for a large scale tournament like APEX; since they have literally a nation's worth of resources, they should easily be able to get together, say, 20 fully unlocked 3ds units (that is, 20 physical copies of the game at all and one powersaves if truly no one on EC can be bothered to unlock things) and set the entire thing up in under a half an hour even on their massive set-up count. It's actually harder to unlock random stage switch in 4 than to set up custom moves, seriously. If all of the set-ups will have every stage unlocked (and they should!), there is not a practical problem to having a custom move system in place. I get a sense they just didn't get around to figuring this out in time, but it's right here so... it can be done.
A few of the other rules are just strange. Why is a Bowser Jr. glitch banned? I won't claim I'm familiar, but is this glitch severely gamebreaking or something? It hasn't made waves in the community at all thus far if nothing else; could someone explain why on that rule to me? Likewise, what's up with the suicide rule? Smash 4 definitely doesn't need it and shouldn't have it (the game mechanics are super explicit that suicide moves are supposed to generally lose), but the way the rules are written, I don't actually understand if it's a rule or not since it refers to a list of moves that doesn't exist so does that mean that zero suicide moves are recognized under this rule? If that's the case (which would be the best possible actual rule), why not remove that wording that doesn't do anything from the rules?
I don't want to just be dismissive; I know running APEX is a huge challenge and that perhaps making rules was a lower priority to other concerns. I can totally understand putting all of the other important components of running such a large national as a higher priority than making a quality ruleset, and the most likely explanation for this ruleset is that they just didn't have a lot of time to put into it and with extremely little time just tried to play it as safe as they could and made a few mistakes. I just wish they'd been way more engaged with the community on this; there are a lot of us who would have been more than willing to help them on the rules by using our time in lieu of their perhaps more limited time.
Of course, it's still pretty far out; this can be fixed if they want to do so pretty easily. The stage list thing pretty much just needs to remove the starter/cp distinction and make Skyloft, Wuhu, and "any other stage they want to make 13 total" legal and it goes from awful stage rules to perfect stage rules which is actually not that big of tweaking and keeps the core character of what they were going for with stage rules in-tact. If they are having problems getting the customs set up but that's their only concern, just let us know and we'll make it happen. I guarantee I can find you guys enough fully unlocked 3ds units to set everything up; just let me know, and I'll get to contacting people and coordinate those resources getting where they need to go so customs can happen. No matter how many 3ds units you guys feel you need to set it up in an efficient manner, I guarantee we can make it happen. The other strange rules like the suicide rule that as written doesn't seem to do anything just need some clean-up, clarification, and explanation.
I do hope, with the rules being out in the open, that we can tweak a bit to make things a lot better. I think the principles that were behind this ruleset are mostly sound, but it was just rushed and messed up some particulars. Just let the community step in and help out on fixing these particulars, and we'll have a super great national level ruleset that everyone can enjoy.