I feel not enough can safely counter it late game to allow it to stay in this environment.
No, I'm not making this post completely to counter that statement you've made, but I've used that as a lead in for this post.
That is a completely overgeneralizing and judgmental statement to make. You're assuming that your team can successfully take out any specific counters that are necessary in the first place, and that works with ANY POKEMON.
What do I feel Deoxys-E brings to the table? It brings something no other Pokemon brings. Are we really satisfied with the entire speed tiers being about outspeeding base 130s or Scarfed Heracross? Since Deoxys-E lacks power considerably more than most Pokemon, it has to rely entirely on type coverage, and since no moveset is going to hit everything SE, you're going to have trouble making one that will consistently sweep the floor with everything you fight. (read: impossible)
Deoxys requires players to strategically sit down and think about a way to take care of something faster, because if you're going to get swept by Deoxys, what are you going to do against a Mixed Blaziken that just used Agility?
Of course, the argument is that Deoxys doesn't need any item or specific turn to stat up, since it's already at that insane speed, and it can work on its power instead by using Life orb or expert belt. Of course, expert belt cuts your sweeping ability severely. If your opponent is not packing the specific types you're planning to take down with your type coverage, I'm sorry, but you're not going to do much, so you almost have to resort to using Life Orb, which will wear you down alongside possible spikes/SR and sandstorm, the former being something that almost all competitive teams will carry, and a high priority attack will take you out immediately. Walls can have a tough time switching in to take two hits if they get outpredicted, but if Deoxys has been worn down a slight bit, a bulkier Pokemon carrying a high priority attack can take it down immediately. Considering Lucario, arguably the most common carrier of a high priority attack, is out there a lot and can switch into any attacks but superpower fairly safely (psychic does 74.11% - 87.23%), it can choose between predicting a switch to Swords Dance up, possibly offering a sweep, or just extremespeeding off the bat to kill.
What I'm saying is, Deoxys doesn't cause the game to be more about stalling, but it encourages teams to find more efficient ways to beat counters and have a fun match all the same. I realized pretty soon after I started competitive battling months back that the best way to counter fast Pokemon was not to try to just get as fast as you can to outspeed, because there's almost always going to be something that can outspeed you. Your best option is to pack bulkier sweepers; pack priority attacks.
The term "mixed sweeper" almost seems like an awful generalization to use on Deoxys. To me, as with most other "mixed sweepers", it plays out mostly in the fact that it has a move to kill Blissey, and then it tries to kill the rest of your team. If it has to come down to 1 v 1, Blissey can easily stay in on you and take your superpower, then thunderwave you. Blissey switches out to something to take your superpower, and you're already down at least 20%, and you're paralyzed. Sure, Blissey is going to be annoying to get in later if SR is up, but it's not incredibly hard to get a softboil in on blissey while something assaults you with special attacks.
I believe I've brought this on far longer than I wanted to, and I've probably done a horrible job at explaining my point due to the fact that I.. really need to go to sleep. I apologize if my argument came out like crap.