Here are my thoughts on the matter:
PJIs are very unlikely to go back to being able to block phase jumps entirely with no drawbacks(yes, even the 2 connected systems with PJI idea).
Let's start the analysis with some numbers:
Current default phase jump power-up time: 7 seconds
Current default phase jump delay from PJI: 18 seconds (250%)
Total jump time under PJI influence: 25 seconds
The general consensus is that 25 seconds is not long enough, so let's see what we can do:
Adding a research that increases jump delay by an additional 50% (so 300%, 350%, 400%) per rank would give us 28 seconds with rank 1, 32 seconds with rank 2, 35 seconds with rank 3 (assuming rounding up). Okay, so that's 10 extra seconds of delay with some research, not bad right? Still, 10 seconds isn't a whole lot of time, so let's see what else we can do.
Why not make PJIs affect phase space speed itself? Phase lanes can be quite long, and huffing and puffing along them can be a grand time killer without directly trapping the hostile fleet. Why not add on the ability to research incoming and outgoing phase space delay?
Here's how I picture it:
[Basic PJI module research] >(next lab)> [Additional 3 ranks of research for total 400% charge-up delay] >(3 additional labs)> [2 ranks to increase incoming and outgoing phase space speed by 200%]
Pros: PJI progressively gets better as you sink more money into research, instead of being a one shot wonder. It does what it's meant to do still, which is to delay the enemy, without creating a grav well death trap.
Cons: Research costs would add up. Some races would get access considerably earlier than others (Vasari), and on smaller maps not all races may be able to make full use of them.
The cons, for me, are actually pretty arguable. Vasari are meant to be the masters of phase tech, so I can live with them having access to the complete PJI path 2 labs ahead of the TEC. This also wouldn't stop people bypassing your choke points, but it would slow it down considerably (35 second charge up, incoming AND outgoing phase space speed reduced by 200%).
There's my idea