A long time ago, I used the GNU PCB tool to design a flex circuit. I ended up having to hand edit the gerber files to get the project done because it didn't support changing soldermask opening. I think they've changed it since then, but it was rough for awhile.
I've used GNU PCB and gschem extensively. While there's a definite learning curve, I've found them very usable and produced many boards with great success. Like you say, maybe you hit some issues that have since been fixed, but this is another datapoint. As for kicad, it came into existence after I was relatively proficient with gEDA, and it there never were any compelling reasons to switch.
I'm pretty much in the same place. I have gEDA symbol and footprint libraries that I like, and the cost of redoing those and climbing the learning curve for KiCAD isn't justified. Many of my friends use KiCAD, and it seems both have issues, just in different places. I've looked at the KiCAD footprint library format, and it is a sad mess. Of course, gEDA's footprint library format also has limitations of probably equal measure.
In any case, I've done many rigid PCBs and one flex PCB with gEDA and never had to resort to hand-editing files. That said, I have written my own footprint creation tools to get exactly what I want. That up-front cost is part of getting either KiCAD or gEDA to yield the desired results.
As in many things about EDA, libraries are the speed bump that repeatedly jars your brain case.
