I think you're very right about my marketing problem :)
On the surface, my website is kinda out there. I built it from the ground up using Rake and some gems as a static site generator. I think it's very cool, and I don't expect that many people will appreciate it, but I'm hoping that one day someone comes along and says "wow, that's pretty cool, wanna help us with this Ruby thing?")
In a deeper way, this whole discussion is very helpful... it's giving me a fresh perspective on how to frame conversations with future potential employers.
And actually the other day I had an epiphany about my marketing. Sure, I chose an odd path, but I've already done so much of the work! I just need to get my random little open source tools in decent, usable shape so that people who'd find them useful might actually get a chance to use them. I need to get my half done work finished and make tutorials about it and get myself out there.
This came after I got a call from a contracting company who told me they were bidding on an interesting job that might be a good fit for me... I was so excited that I stayed up all night and finished like three old random projects at the same time, just so I could put more stuff on my portfolio. It was a wakeup call, affirming that there actually just might be some cool work out there after all... so get your shit together!
I have the 3 primary skillset problem you describe and have a decade of "founder" experience. I thought the breadth of experience and technologies would be impressive, but I think it just confuses most employers. It seems counter-intuitive to intentionally not mention your skills on your resume, and admittedly a little ego-deflating.. but this actually makes sense.
I was heading the direction of very focused resumes. I've also landed a low pressure founder role too, so that's nice.
If you have 3 primary skill sets you should have 3 focused resumes.
If you want a position that requires a generalist, the only/best fit would be founder. In almost all other circumstances, companies hire for a problem and not general optimizations. Even if they need a generalist.
I would posit that you have a marketing problem and not a skills mismatch problem. The noise to signal ratio on your resume may be making it seem to not match any position.