Quoting SgtHydra, reply 22A magnetic cloud has pretty much the same affect on my plans as a plasma storm. Neither one would ever turn the tide of any battle
On the contrary. A magnetic cloud can easily turn the battle away from a player who likes using ships with abilities - especially Vasari late-game with Overseers and Subverters, or TEC with Hoshikos.
And the effects of a plasma storm are also very significant in all parts of the game - completely negating strike craft on both sides is huge. I played one game where I had 3 carrier caps chasing a damaged enemy capital ship. The enemy escaped into a plasma storm and was able to kite around enough to survive, since my bombers couldn't attack.
Granted, there are considerations to make (it's fairly pointless to send a bunch of flak frigates to defend a plasma storm, for example), but there is no real "umpf" to most of them. Sure, they all do have a bonus and it can be useful, but that's really only rarely.
The current bonuses should be left in place, but each should have a new bonus that encourages players to think strategically in response to an opponent's own strategic thinking.
Let's take your example. Your opponent went into the plasma storming thinking "he's got 3 carriers, all of which would be useless in there." AND THAT'S GREAT!
But... you should be at the same time thinking "okay, he's going into the plasma storm to avoid my carriers, but I'm going to use [insert plasma storm's new ability] to my advantage. It'll be close, but I just might pull it off."
Strategy should be like that, not the one sided "oh well, can't use strike craft here so he got away" nonsense you were forced into. The ground you fight on is important. Vitally important. The one who picks the ground you fight on has the initial advantage, but so long as you can adapt to the battlefield and make it your own, you can still be victorious. And you can always adapt to your battlefield. That's what made D-Day so successful. For millenia, armies were always defeated when they had their backs to the sea, until June 6th, 1944. It wasn't because America was involved and thus victory was assured or that the disadvantage of being boxed in on all sides had disappeared, but it was because the Allied forces adapted to the terrain and specifically targeted the weaknesses in the German defenses that gave them victory.
Whatever new bonuses are handed out shouldn't suddenly make magnetic clouds and plasma storms the center of all battles from now on. Instead, they should give an experienced player a chance to adapt and emerge victorious.
It just needs some nuance to make these non-planetary slots interesting to fight in. Because really, they should be interesting to fight in. All the cool stuff in space operas happen in asteroid belts or nebula. Cause that's where tactics can overcome basic firepower or numbers.