I've had the same dream, just never actually got around to it.
Most of the recommendations above are for dev boards. Since you said "from scratch" I'd assume you want to start with a single DIP processor chip and not buy a dev board. In which case I would very extremely super recommend you stick with something like the usual suspects you listed in your post. They are popular because they work well for such a task. You can overcome the need for more I/O lines with multiplexers and demultiplexers.
Suppose you did find that "perfect" CPU that does everything you want, and has the exact number of IO lines you want. You are not going to find anywhere near a smidgen of the support you'll find for the popular processors. You should very easily be able to find old used books on E-Bay, Amazon, etc. for just pennies that show how to design a complete system using those processors. Not to mention websites, compilers, and other people doing the same thing.
If you go with anything else, I think you're going to regret it deeply. You'll spend more time frustrated over lack of support than you would overcoming any technical issues you have with those processors. Plus, since people have already designed entire computers with those chips, you know it can be done. With anything else, there's always a chance you'll hit a brick wall.