A Combination of Albative Hull Generator + Ablative Plates + Multi Layer shields + Multiple shields should honestly be standard by the future.
Instead of a battle taking minutes to finish off a StarFleet vessel, it should extend out to be like a super long wrestling match that can take 20-60 mins to finish.
Don't forget all those fancy new technologies (in TNG time) like that fancy "multiphasic shielding" or whatever is was that that Ferengi scientist discovered...and then there is "regenerative shielding" and even that Romulan cloaking that let them phase through solid objects.
And by the end of the 24th century we had all sorts of propulsion advances either realized, or on the horizon. Voyager had "variable geometry warp drive" (apparently so did the E-E, but it was never mentioned) and the Slipstream drive. And by the time of the Enterprise-J they likely perfected things like co-axial warp and artificial wormhole generation that was being researched in Deep Space Nine.
And the E-J also had Xindi crew, so there is that Xindi vortex tech they might have incorporated.
By the very, very least, the E-J has slipstream. By the very least.
I kinda imagine that by the time of the Enterprise-J, Starfleet probably has some very...flexible...technology. Like the E-J may have *multiple* FTL propulsion methods available to it. Perhaps some sort of, I dunno, "Multi-Axis Warp Drive" that can generate something like Co-Axial Warp (what even happened to that tech, btw, it was there on Voyager one episode, and gone without explanation the next...?) but could also be used in standard warp ans slipstream/transwarp and possibly even channel energy through the deflectors to generate wormholes - which might not be commonly used methods, but would all be there for unusual circumstances. And be easy to access as flipping a switch or hot swapping out components in engineering.
So if in episode 22 the ship's co-axial warp is down for [TECH] reason, they could switch over to the transwarp coils and 'limp home" on slipstream.
The problem is that the more and more you project Star Trek technology to the point it was headed in by the end of Voyager, the tech becomes basically magic, and there is almost nothing you can't do...so then you have to start envisioning all sorts of convoluted and non-sense sounding technobabble reason why X-technology won't work in this situation. (Something they seemed to actually run into on Voyager near the end.)
Which may by why the last 2 TV series and the last 3 movies have all been set in TOS and earlier timelines.