This will be my first post to the forums.

Loving the game so far. I have a few suggestions for 1.03.
Let me be the next in a long line of folks to mention the PJI. In its current state it is worthless. Just add my voice to the deafening mass of other voices saying the same thing.

Personally, I think a PJI that affects an entire gravity well and fully stops non-ally's phase jumping is not overpowered. They can be destroyed quickly anyway, so this would serve mostly to punish those who disobey a prime tenet of war and attack without scouting first (I do this myself, but only because in this game right now I can get away with it). I'm also a big fan of the "phasing cooldown" idea that has been mentioned in the past, so that moving ships right through enemy strongholds is time consuming and a little costly, even without PJI being present. The defenses should NOT be able to overpower offense - but as of right now you can't even THINK of defending your core worlds with "fortress" worlds on the front lines, because the opposing fleets can race past all defenses and hit your soft underbelly with impunity.
I do NOT think basing fleet supply limits on planets owned is a good idea. This will simply bring the game to a decisive close earlier in mid-game, resulting in a longer late game boring steamroll effect. Why? Because, especially on smaller maps, once on side has a decisive edge in planets, they will have both a decisive edge in economy and fleet supply. This is not always the case in real life anyway and should not be the case in a game. In other words, losing players should have at least some chance of a resurgence or why not call the game halfway through and quit? The Fleet supply "ladder" techs should be spread out less, though, with more tiers, perhaps leading all the way up to a huge fleet and 95% income reduction at the top end. Because the cost of ships and research doesn't change, 95% income reduction might be viable on HUGE maps for desperate players, and let's face it - huge maps are where the logistics techs seem to make no sense as is.
I'm not sure what the fuss is about regarding seige frigates. They made me scratch my head the first game I played, and now they are usually non-issues, except when an opponent ties my fleet up somewhere and then expertly smacks me from behind with seiges at a not yet fortified planet. When that happens though, it's only right that my planet gets destroyed - my opponent did something sneaky and I wasn't prepared!
There is also another aspect of logistics being ignored that may make the game much more tactical - and that is how many ships can be stacked in one system. Only allowing a limited number of ships to be stacked in a given system without some tech or support unit or structure would add another layer of logistical complexity and would make huge "victory fleets" less of an issue until late game It would make multiple fronts and hit-and-run strategies more viable, because making a hit-and-run somewhere wont necessarily mean your "giant blob o' ships" is now smaller than your enemy's "giant blob o' ships" at the main point of contention. It would also be a HUGE alteration to game play - so I don't expect it to be taken seriously.