In considering the topic covered here, there is definitely a weakness in the game with the way an opponent can completely circumvent logical defenses and the nature of the positioning of planets and the jump lanes. Implementing a jump-around or edge-jump sequence while a ship is 'passing through' would be excellent. Perhaps an advanced jump drive that can do the former at higher technology levels.
A big problem, as others have pointed out, is how the enemy can jump to the edge of your system, jump again to the system on the other side, then jump back, thereby bypassing any defenses you've put in place. I've been dealing with this by building respectable defenses by every lane -- but with high maintenance, this isn't always a viable option if you're waging a decent war. So my strategy has been to focus on strategically significant systems (choke points). But, until I get a phase jump inhibitor in place, these strategies are basically meaningless.
I'm not recommending changing the game mechanics too horribly, but having the option of some additional items would be very nice. I'm not the first to suggest these, but I feel these would contribute to diversifying the strategic and tactical options available to the player as well as providing different approaches during different phases of the game. I'm definitely seeing some nice mod options with features like this, too.

1. Ship-based phase jump inhibitor, or perhaps an early-game weapon (structure or vessel based) that delays jumping for a time.
2. Some ships cannot jump without structure(s) at start (and finish) (ie: Babylon 5)
3. Construction ships that can build structures in both star wells and planetary wells