The F430 is billed as an "evolution" over the 360, as opposed to a "revolution" which would be the relationship of the 458 Italia to the F430.
I too had this same dilemma before I bought my 360 Spider. Ultimately, I could afford either one (and the maintenance for which ever I chose). My wife, however, felt more comfortable with the up front investment in the 360, so she asked me to buy the 360 instead of the F430. Do I like the F430? Yes. Do I miss not having one? Well, you can't really miss it if you don't know.
The F430 is an epic car. There are some pretty significant technological improvements with regard to the F1 system as well as the now-standard Manetinno, which I think is really cool. But, I love how "analog" my 360 is, in an age full of digital cars. I regard my 360 as "simple," but in a beautiful sort of way.
As far as maintenance, you're pretty much named them - belts versus chains. They both suffer from the same exhaust system weaknesses in the headers/precats. At the end of the day, either one is a Ferrari, so they're going to be "quirky," but that's part of the charm and part of why we love them.
With regard to years, the 360 Spider was virtually identical over the production run from 2001-2005. Upgrades were made to the F1 TCU, which can easily be remedied on an older car (my 2001 Spider has the newest non-CS TCU). For the F430, the general consensus is that MY-2008 onwards are more remarkable because the CCB's were standard, and there were probably a few other minor improvements I'm forgetting. The CCB's were the major improvement, I think. That said, if you don't care about that, there's nothing wrong with earlier F430's.
The manual transmission is inherently more reliable than the F1 gearbox, because there's less electronic equipment in the system (fewer parts = more reliable). That said, a lot of people really like the F1, and you'll recall that F1 cars make up the majority of the market. There's nothing really wrong with the F1 system, other than it can go bad, and if it goes bad, it's expensive. That's par for the course with Ferrari.
Ultimately, you need to try and drive both. I did that. The drive of the F430 was superior to the 360 IMO, but the 360 has other endearing qualities which can be highly subjective. What is NOT subjective is the substantial difference in up front costs. You'll likely NEVER make up the cost difference in reduced maintenance if you buy a 360 over an F430.
I'll end it like I always do. Both cars are amazing, you can't go wrong. Go drive them and the decision will be a lot easier for you. Good luck.