Unfortunately I didn't get as much time on the 2/2.5 builds as I did the original beta 1, but I'll write on what I can.
Starbases
The changes to weapon banks having several targets was a gigantic improvement to starbases. It's great all around. They feel (and are) powerful enough when fully upgraded.
However, the change to time taken to deploy in the hostile grav well I feel was increased too much. It's now prohibitively long that really the only time you might use one offensively is if there's no hostile fleet in orbit. Which, incidentally, is when you really don't need to worry about a combat deployment. I think it should take longer than in beta 1, but still shorter than it is now so that it would actually be possible to defend a starbase under deployment.
Besides that, I can't say I have any other bad things to say, they're just that awesome. I'm worried about the new Meteor Storm and hull damage if it was left without a target limit, but I have not had the chance to try it.
As far as bugs, here are 2 recent 2.5 bugs and starbases:
https://forums.sinsofasolarempire.com/338972 - Queued upgrades bug out
https://forums.sinsofasolarempire.com/338786 - Weapons firing on single target
Mines
The new mines are much better than the old ones. The limit of 150 seems about right given the area you can cover. So you can't just mine the whole grav well easily, you have to be somewhat selective.
As far as deployment, the Vasari ones I think could use a little adjustment. I like that you select a deployment area and it spreads them out, but I think the area is too small and there are too few mines. It takes a while just to queue everything up. I wouldn't complain if the number of mines placed and the radius increased, with the cost scaling proportionately. I'm also a bit of a neat freak, and the TEC minefields look nice and even while no matter how hard you try to even out the Vasari ones, it's all in clumps 
There's also some bad behavior when queuing mine placement. The TEC ones are a "building", so I can understand needing credits to place each one. The Vasari mines, however, require you to have sufficient resources for each queue of the ability usage. Ideally, I would like to be able to select my Ruiner, queue all the mine placements I want without having to babysit it to make sure I have the resources on each queue click. Needing enough on the first order is good, but after that it'd be great if they ignored current resources for queueing. It's already smart and waits for you to have enough before it actually casts it, so that works out nicely.
There's another issue that I'd like to bring up again: deploying mines at jump-in, and ship turning arcs. With the limit of 150 it's now harder to mine every jump in point, but it's still possible. It only takes a few mines to knock out the bulk of the fleet (light frigates, long range frigates, and most supports), rendering the remaining ships not only barely hanging in there but also useless for any serious fighting. Against a player, this isn't terribly bad since the chances are they can find a spot to jump in that's clear. But the AI will never be that smart, and it will be really easy to defeat large AI fleets with just a few mine placements right at jump in. Then there's ships turning. Quite often you can't simply keep your fleet back and let your scouts do the sweeping. There might be a starbase in system with fighters and other hangars, or there might even be a hostile fleet. If your scouts go forward alone, they'll get torn to shreds. But if you send your fleet forward, the ships simply cannot be allowed to move, giving the defender an immense advantage. Its ships are in no danger from mines, but most of yours cannot reach their back line to take out the LRFs and support ships. And forget about trying to retreat, as they'll make wide forward turns and detonate all the mines.
To solve both of these, I once again propose that the scouts' mine detection ability also disables abilities on the detected mines. That way, once the mines are spotted they can't be triggered until the scouts leave range or get destroyed. This would actually allow your ships some room to maneuver without watching in horror as they all get blown up with nothing you can do, and it would also solve the jump-in issue.
And, while we're on the topic of AI - they don't actually put scouts into their fleets, so they are completely helpless against mines. They don't even try to avoid them. I've seen a friendly AI plow right through a field of hostile mines when trying to retreat, losing pretty much everything. The AI has to put scouts in their fleets and it has to try and disarm the mines. The scouts' formation in the fleet could use a slight move up to the front. They should be behind the front line ships, but still a little forward of where they are now so that their detection hits a little bit further in front, giving your ships time to shoot them down before running into them.
Defense Busters
Their change to using weapons rather than abilities help with managing them, but they introduce another problem. Even though they prioritize buildings, if you jump into an enemy grav well with their fleet you either start hearing lots of really loud "raze planet" explosion sounds and get blinded by having a bunch of your ships lit up with them, or you sit through a constant stream of blue particles going every which way. Large battles can already be messy, and this adds to it. However, this way is still better than the old ability-based, so I wouldn't want to go back to the old way.
But, can you do something about the Ogrov sounds? It works ok on the Marza's Raze Planet because you don't hear 20 of them. It gets really bad when there are a bunch of Ogrovs constantly firing - it's a loud sound that drowns everything out. Making it quieter would be ok, or I wouldn't complain about a new sound that's less of a contrast to everything else.