I agree 100% with ksand24. The rules are easier for EEA applicants, so I would follow them. Plus if your end goal is citizenship, I think if you follow the outlined procedures and do things by the book (family permit, residence card, permanent residence card), the whole process is much, much easier.
The only thing I can add is the EEA2 applications do take 6 months, sometimes longer. If you need your passport back to travel, you can request that it be returned to you without your application being cancelled. But the practicality and logistics of actually sending it back may prove difficult and it the end it will ultimately delay your application in my opinion.
When I applied for my residence card, I was told I could easily request my passport back if I needed to travel. It made the process sound simple. It wasn't and in the end I had to get an emergency passport from the US embassy. When I returned to the UK I was stamped with a code 1A in my emergency passport (Note I had copies of all my application paperwork with me for back-up.) It was a risk and I don't recommend it. Technically, I should have applied for another family permit was I wasn't out of the UK for long and didn't have enough time to apply.
If your EEA partner is self-employed, they may want further evidence that he's paid his taxes. With my application, since six months had gone by I had to provide proofs that my partner made additional payments to HMRC.
Good luck!