Okay, if I had to make a banlist to try and make modified healthier, I would probably start with a lot less bans and see where it goes. I can see weeding out OHKOs, at least "easy ones", as a good starting point. So I would start by banning just these:
G Booster
Yveltal EX
Black Kyurem EX (Black Ballista)
Rayquaza EX
These are the only good cards in the current format that actually just OHKO everything, even Megas at times. Yveltal *might* not be as ridiculous without its extra 30 damage from Laser (see below), but I think either Dark Patch or Yveltal needs to be banned/restricted somehow. I purposely left Keldeo EX and Mewtwo EX on the list, because they require a rather absurd amount of Energy to function, which makes them easy to KO on a counter with another Mewtwo EX, Leafeon or Deoxys EX. Loading them with Energy just for an OHKO on an EX will always be a risky play and I believe better players would prefer to make more conservative plays.
I also think either Hypnotoxic Laser or Virbank City Gym could do with a ban, probably Hypnotoxic Laser. The reason I don't think you have to ban both is because keeping Laser allows you to play cards like Ninetales or Raticate should you want to and still get a good use out of them, while keeping Virbank lets you get milage out of a card like Amoonguss. Alternatively you could ban decks that play one from also playing the other, a la Sycamore/Juniper. I think the 25% chance of an extra free turn on its own is kind of powerful, but not worth playing without also getting an extra 60 free damage out of it (three times 20 extra between turns) unless Virbank is really popular.
I think other flippy, extremely powerful cards like Crushing Hammer and Catcher are stupid, but I'd prolly not ban them right off the bat. *Maybe* Sableye + Hammer is worth restricting, but once again that's a maybe.
I would ban Tropical Beach for price reasons in a heartbeat, but I would like to keep it around for balance reasons. Honestly, since this is nothing but an unofficial metagame, there is no reason not to allow Beach, since that'd be mostly played in casual settings (proxy becomes an option) or online.
One card that is really hurting potential nowadays is Garbodor. While aggressive decks with active abilities (such as Genesect's Red Signal, Exeggcute's Propagation, the Rain Dance abilities, etc) can sometimes get by with Tool Scrappers, any deck that needs their abilities over the course of the game simply cannot run enough Scrappers/Megaphones and remain consistent. I'm talking about cards like Mr. Mime and Klinklang PLF.
I'm aware that this banlist leaves a lot of powerful cards still in the format. I don't think the current draw supporters need to be touched, because we have no better consistency engines. If you really want to slow the game down significantly, you would have to ban basically the entire format, not just parts of it. All I've done is try to eliminate the easiest OHKOs as well as the most poisonous cards (Garbodor and Laser).
Plasma is virtually untouched aside from losing the Laser option, but I'm not too bothered with it because there's a lot of cards in the format that aim to counter it: Silver Mirror, Enhanced Hammer, Sawk, Drifblims, etc.
Virizion/Genesect lost nothing but G Booster, just like in vaporeon's OP, but since I left Superior Energy Retrieval and Professor Juniper alone, cards like Emboar and Flareon have an easier time beating it - although Emboar lost Rayquaza EX. Pyroar also still exists.
The Yveltal variants are gone, and Dark Patch decks would have to go back to Darkrai, Sableye, regular Yveltal and Absol. I think this is a manageable but still potent deck. The last time we saw straight Darkrai do well was a long, long time ago, but a lot of its problem opponents (OHKO cards) are gone. On the flipside, Laser is gone.
One interesting deck that can still OHKO everything is Weavile, which finds itself no longer restricted by Garbodor.
That's how I'd go about it if I made this kind of a format.