That's generally how I build gateways too. Not sure if it's a good or bad idea, but I usually have a single main shipyard system one jump from my home system, which has a mega shipyard and 6 shipyard spaceport. I stick a gateway in that system, then one about a jump away from each border station, and if my empire is particularly massive I'll sprinkle a few gateways in pockets. That largely eliminates piracy because of the overlapping trade protection and short distances back to my home system, while allowing rapid deployment and reinforcement of ships to frontlines.
I've always wondered if it was better or worse to build the gateways in the border systems with bastions. If I lose that system then I lose the gateway, but if I lose a bastion system I'm probably losing whatever is behind it anyway I guess. Doing it a jump away lets me share a gateway to several bastions sometimes though.
I do like that gateways change things up in the late game and generally make the game more convenient. Jump drives help a lot too, but are more situational. However, gateways do also mitigate the biggest drawback to big empires, as ventuswings pointed out. I have a bit of a love-hate relationship with that. I like that fleet positioning matters... until it inconveniences me, at which point I hate the fact that it takes so long to move ships around.
Regarding the crisis: this is one reason I almost prefer to not have L-gates in my empire. If the crisis ever reaches the L-cluster you just cannot keep these systems. They'll pop in, zap the station in 2 seconds, convert it to one of theirs, and pop out. Well, this and the fact that the AI will unleash the Grey Tempest when nobody in the galaxy has even 10k fleet power. I've had crises last 100+ years, but those were cases where I had a hard time reaching them due to idiot neighbors who wouldn't open up borders to me so I could fight the crisis. I've never, ever, seen one of the mechanics trigger where the crisis has spiraled out of control and other factions show up to help / make it worse.