My guess is that they'll stay in the future. That way they can do new stuff, not have to worry about gaggles of complaining "fans" who want to do nothing but pick holes in things, and can actually move forward. New stuff to explore and all that.
Destroying Leland did not destroy Control [MENTION=2518]Derren[/MENTION]. Control was destroyed by Star Fleet HQ at the end of the show. All they destroyed was a local instance that was controlling (heh) the fleet. Can't pilot all those ships remotely with all the subspace relays down now can they?
And, I'm sorry, but that fight scene was AWESOME.
Sure, the bulkhead thing was lame, but, let's not forget, they did actually tell you that with the bulkheads closed, they'd still lose a big old chunk of the ship - which they did. With the bulkhead open, the whole ship would be lost. Does make you wonder what they make the bulkheads out of.
And, as far as the shuttles go, I would assume that they did have the shuttles - they did just fight a major war against the Klingons. Every Star Fleet ship would still be geared up for that. Which means lots of shuttles. That's not even breaking canon if you're a Star Fleet Battles fan. As far as using it against the Klingons, how often did we actually see a battle with the Klingons after the first episode. A couple of engagements, but, nothing serious. And, again, they did say that they were converting all shuttles and pods to make fighters. Nice to see them actually use the technological capabilities of the ships for once instead of ignoring it.
The question you should be asking is, if Enterprise D or any later ship had replicators to the extent that they do, why didn't they ever do this tactic before? Makes pretty much zero sense that they didn't. DS9 had an entire station at its disposal and never bothered making so much as a skiff. The Runabout's were delivered from Star Fleet. Why didn't they just fabricate a couple of thousand of those to deal with the Dominion.
Oh, right, we're supposed to talk about Discovery plot holes... all the other enormous plot holes in other Trek's we're supposed to ignore because Discovery sucks and all the other Trek's were examples of perfection.