Unfettered Phase Jumps - Why is this so expensive? Phase Jump Inhibitors aren't exactly common, and even then scouts are so cheap that losing one is hardly game breaking. This should be tier 2-3 research at most. (issue for all factions, I won't list this one again)
One of the purposes of PJI's is to prevent scouts from getting a few jumps behind your front lines to see what you're cooking. So in that sense I do think it's the right decision to put it high on the tech tree, but I also think it's a tad expensive. Maybe keep its current position but lower its cost. It's nice that most techs have a standardized cost based on their tier, but if it's justifiable exceptions should be made.
Anti-matter upgrades - These are pretty damn low on most people's priority list. and yet even the initial upgrades are pretty pricy. Shifting these a little lower would help out carriers and make various defencive structures a fair bit more usable. (issue for all factions, I won't list this one again)
Totally disagree; this is one of my top priority researches. Now, I tend to go a bit heavy on capital ships and therefor have lots of powerful abilities to feed with antimatter, so maybe this is a bit specific to my playstyle, but the fact still remains that this upgrade is anything but useless. Now, it does bother me that I need to put up four labs to get the TEC upgrade. I mean, I may as well go for heavy cruisers if I've already got that much infrastructure...
High Efficiency Jumps - 1600$ 300m 475c for a minor reduction in jump antimatter cost? Seriously? This one needs to be a lot cheaper.
Lifesaver in the late game, but still very rare to get it. If you're playing cat and mouse a couple jumps can really whittle away your antimatter and reduce the power of your caps and support cruisers in the coming battle. That said, it's rare you can shell out that much cash. I'd agree that it could use some help, but it's not the poster boy for underpowered techs.
Beam Weapons - Asking an awful lot for something that ONLY benefits one cap ships and starbases.
Agreed. I've never researched this.
High Yield Warheads - Too expensive and too late for something that is far more useful mid-game. Piling on the bombing damage and being an ass on large maps might actually be effective if this wasn't tier 6.
It's weak, but not worthless. I don't think it's a huge issue.
Catastrophe Recovery - This is useless. If you repel an attack before the planet is destroyed, then the health is probably going to recover before they can attack that planet again.
Not entirely. If you can force the enemy capital ship to break off bombardment for even a few seconds, a planet can regenerate hundreds of hit points. However, I do agree that these scenarios are fairly rare.
Basic Crew Training - Tier 5 for this? If you have the money to research this and buy levels for your cap ships, you're winning anyways.
Agreed, too late in the tree, especially when compared to the other factions. That said, being able to pay for level 4 is quite useful for raising caps in the late game, but this is too far up the tree.
Wave Cannon upgrades - Way too expensive. The Enforcer is already the worst heavy cruiser, and the cost of weapon upgrades for them doesn't help.
Totally agreed.
Colony Pods - there's nothing wrong with the research itself, but the actual cost on the starbase upgrade is never worth it. Trade ports cost less and yet give as much of a boost as TWO colony pod upgrades.
Totally agreed.
Of course, you missed some pretty glaring ones:
Advent Beam Range
The only Advent beam unit that has any real range to boost is the Illuminator, and even then it will never outrange anything significant. Waste of cash.
Advent Resource Focus
Seriously, you need to stack both of its higher tech level upgrades and multiple loyalty boosting effects on a planet just to make this competitive with its trade route form... and by the time you can do this your trade route is probably so long that it still isn't viable. This needs serious boosting because right now there's virtually no practical situation where it's ever viable.
Advent Increased Hanger Capacity
Seriously, not good enough to be worth our time.
Vasari Bombard Range Upgrade
Thousands of credits for a 10% increase in bombard range? You're kidding right. I've never actually seen a case where this increase of range would actually have been useful, much less worth its massive investment cost.