@loudkirbyking
Yes, there will always be issues with a ban list. However in yugioh, their list is made with money in mind to force players to play the new, promoted archetype. Their list is not really about the health of the format like it once was, since they keep putting the same effects on the new cards that got banned the format before. However with the list in Pokemon, things should only be banned IF they cause imbalance within the current and foreseen formats. There will always be tier one decks but if that tier one deck makes the format into a play or counter format, it will be looked at. If that tier one deck does not do that and is tier one because of its synergy and other decks exist that can beat it, then it may not be looked at if nothing is broken or unbalances the format.
You do bring up the point of cards being looked at. Perhaps its better to have more catchers in the format but we have to remember that basic pokemon (both non and EX) are still powerful and a catcher heads flip can still cause problem. It was a few years ago where people lived or died to reversal flips. Maybe 2 are good there. With BW-Extended, we'll have to create a second ban list for that format as well since things like zekeels will become a problem. Everything will need to be tested but once a solid list is constructed, everything should be fine until something needs to be looked at.
As for your last point, its better to test these two things together because what may be broken or overpowered by itself may not be broken with a side deck since counter options open up.
The issue now is that you assume pokemon isn't into money and/or won't do the same thing. Who's to say Pokemon won't make another Evil Ball attack on a new type like Fire types or Water types? Plus if your goal is to create a format where the tier one decks don't have to be specifically countered by x techs or you lose, then you'll find a lot of bias in trying to make this list. People will begin to complain about X deck not being playable because of Y, and whine that Y needs to be banned. Even with a banlist and ignoring bias, think about explaining it to the younger kids Pokemon is marketing to if they decide to implement something like this. Tell a 7 year old that the Mega Charizard he pulled, he can't play because it's too good. Sure, Yugioh has the same problem but it has a difference. It's not aimed at kids nearly as much as pokemon, but more for the teen market from my experience. That, and cards are from every set so you can't tell a kid that the Yugi starter deck cards he got from a friend aren't good, but you can tell a kid that the base set stuff his cousin brought him aren't good. It's limiting a limited format even more, which is a bit sad at first thought and really sad when you realize that the format would need it to exit this big basics era, or something else big.
But nonetheless, back to card issues. The one thing you did not mention was the issues with Genesect again. Even with Flareon and Ho-oh, realize this issue. Firstly, Genesect is much more consistent, especially with Virizion not even being limited. Secondly, the cards Flareon needed, namely Superior energy retrieval(Iffy for this deck, but it's the only other item discard card besides UB and gets energy out without super rodding it) and Juniper/Sycamore to get more pokemon in the discard are now limited. Sure, Ultra ball and Comp search are there, but you did just cut out the main supporter of that deck to 2, and a potential item. Though don't quote me too much on Superior, I haven't played Flareon much myself beyond seeing a few lists run it. Much less, you'd have to get 2 Eevees down just to avoid the red signal into megalo cannon for the OHKO. And it can still OHKO the Flareon while the Flareon needs 5 pokemon and muscle band or 7 pokemon in discard to revenge. Running Garbodor works though, right? Not really. You can either red signal it up easily, play a startling megaphone if it has a tool, or use the one Lysandre. And you might be thinking, 'I can get another one out', but it's only a 2-2 line. Every time I've played Garbodor, and seen people play Garbodor, it's HAD to be a 3-3 line because of just how easily the Trubbish and Garbodor get knocked out and targeted due to Lyssandre, catcher, and red signal, not to mention prized cards. It takes 2 Garbodor, or 1 if one's prized sent up to stop that quick. And now you might think of Sacred Ash or Super rod, but is Flareon REALLY going to be getting pokemon out from the discard much? Is it worth shutting down red signal to kill 30-50 damage when you all ready have troubles getting it down there in the first place? And one more thing that truly ruin this match-up. Plasma Frigate. Sure, counter stadiums, but what stadium would Flareon run? Frozen City?
As for Ho-oh... That's more iffy. The issues with Ho-oh are the same with Flareon. Milling cards just became a lot harder due to Juniper limits, plus Plasma Frigate. Unless you want every fire deck having to deck in enhanced hammers and stadiums to deal with VirGen, but that's 2-4 card slots against arguable your best match-up. Still overcentralizing.
Of course this matchup is mostly theory and just working off lists from this potential new format, but it makes logical sense. Yes, it can go the other way if Flareon gets a great start, but the fact that a deck that should autowin against Genesect still has issues, I'd say that it's a sign that the banlist needs some tuning to prevent this. If you slap every tier 1 deck on the wrist but 1 that you lightly poke, which one will come out on top? It tends to be swayed a bit more towards VirGen than other decks.
Lastly, this is either side. In the first place, if you want these implemented, not a lot of people would want both changes at once. More people prefer to experiment with one change before going onto another. On the other hand, you are right in that some combinations would only be broken with side deck. However, some wouldn't need any banning without side decks that would prevent people from playing if you implemented both. This is more personal opinion, yes, but at least if you were to bring this to me I would tell you to only focus on either the ban list or the side deck at first to keep the changes more simple and calm for players who want to get into a new format. But hey, to each their own.