kingisaaclinksr, glad you're enjoying it so well and thanks for the kind words. I'm really pleased with how this is shaping up, too.
Guardians getting stirred up by scouts should indeed be fixed. We've seen no evidence of them being stirred up by that specifically since 3.717, in 3.718 it was all devourers to our knowledge. Please correct us if that's not so.
Regarding the laser guardians in particular, you need to use siege starships or similar on them. Every guardian (and indeed, every unit in general now) doesn't have a core triangle unit counter, but it does have a counter somewhere in all your new unlocks of starships, turrets, etc. Generally a starship will suffice. If you try to play without starships now, though, you'll get eaten alive most likely. It's a shift for me, too. Of course, depending on your bonus ships that you unlock, you might have more or fewer starships actually needed in terms of counters for things like guardians, etc.
I just got smeared by a fleet of MkV Guardians, some Zenith Starships and a ton of other support units. I just had one unit peep into a wormhole and they ALL came seeping through like crazy for the big win. My main support fleet of 1,300+ ships MkI - III's were all destroyed in about 15 seconds. I then watched this mass of about 400+ MkV ships devour each planet in about 35 seconds each...then I lost.
I don't think the Guardian hostility thing is quite over yet... 
If this wasn't a scout, then this is exactly the intended behavior. They are very, very hostile except to scouts. Poking your head into an AI planet that is high level with anything but a scout is a very dangerous thing to do, like poking your head into any enemy encampment in real life. Fear the AI.
I haven't thought about this with transports too much, though. Any thoughts on how that is working for the moment, anyone? Those might need to be given the same immunity from enraging the guards that scouts have.
Generally speaking, with the lower-level planets it should become self evident to players that this is what is happening by the time they reach a mark V world. By the time you reach the really high level worlds, though, this becomes a very real danger. Of course, if you're using an older savegame where you already have proximity to those sorts of worlds, then you wouldn't have the opportunity to go through that discovery process in a safe fashion, if you see what I mean. It's not supposed to just obliterate you without warning, you're supposed to instinctively know not to prod that particular hornet nest without care by the time you reach one that's so deadly. But existing saves, etc, can really mess with that.
