Cloaking: cool, but the AI has enough problems handling surprise attacks as it is, if you ask it to handle cloaking too it would die a horrible death.
Multiple sensors: you would just have two cargo ships full of sensors sitting in one tile instead of one. Fun idea, but useless gameplay wise except making the AI put more effort into AWACS, which it doesn't even do now.
Huge weapons that toast planets: Terror Stars... it might come back, might not. Probably not. Because...
Planetary Bombardment: Again, fun idea, but would kill gameplay. You'd have a massive fleet fly by their empire and just toast EVERYTHING in it's path. There's no way to intercept transports. Basically if you're weaker than someone, then you have ZERO chance. Think Imperium Galatica II (It's a fun game, but it all boils down to creating an "Ultimate" fleet and going about thrashing the other guy's planet one after another after another after... etc). Just throw strategy out of the window now, it'll be a ship pumping game all over again. The problem is, the amount of time it takes for someone to build a planet is way too long compared to the amount of time you can reduce them to ashes, so the first player who comes up with this ultimate fleet will always win. Where as, if you force someone to bother capturing a planet, you might be able to retake it afterwards.
Ion Frigates: resize your guns to REALLY BIG and stuff it on a tiny ship.
Supply Lines: This is actually interesting, but imagine what it would do to the gameplay. As if the AI doesn't have enough trouble guarding it's troop transports, if you could strandle their fleets and take it over... my god.
In summary: While your ideas are interesting, most of them will probably never see the light of day, simply because they would make the AI a cakewalk. Adding any of these features will mean massive AI changes, that would take months to work out. Others, like Planetary Bombardment, while a nice sensical feature, would just kill the game completely.