Definitely take both types of car for a test drive. I've driven a few MX-5s, and can tell you not to get the Mk3 MX-5, it doesn't drive well at all. Apparently if you lower it and get a different geo setup it drives well, but all the standard ones I drove, drove poorly. The Mk3.5 though is an exceptional car, truly brilliant. Are you sure you want an auto though? Roadsters are more fun with a nice manual
Basically the MX-5 is more fun if you want to go down the country lanes. The suspension is much smoother and it's the smaller car for the narrow lanes. It's a very 'fun' car that you can't help but smile in, even the little 1.8 is quite fun with a very willing engine. Gearbox is notchy for my taste, but it's better than the vast majority of manuals out there - albeit unlikely to be better than your Honda's. I've found Honda gearshifts are wonderfully rifle-bolt in their action. The MX-5 is awful on the motorway, you're revving it at ~4k just like an S2000 at the 70 speed limit. It's also very noisy inside (wind noise mostly) at over 60mph - my Z4 roof down with the deflector in place and windows up is barely noiser than the MX-5 roof up. Don't get me wrong though, it's not unbearable or anything; just tiring.
The Z4 is completely different, it sacrifices a little rawness to gain a lot of refinement - you can very easily cruise for a 1,000 miles and then take on a twisty road at speed. Much more bootspace too, much more. The 3.0 straight 6 will absolutely muller the 2.0 in the MX-5, there is no comparison at all. It's a larger car which makes it arguably more comfortable too, although I'm average size so I found both equally comfortable. maxman mentioned running costs - if I'm honest the running costs between the two are not likely to be that different. The MX-5 gets poor fuel economy for what it is (much like the 2.0 Z4) so the difference won't be substantial - although the auto will decrease your mpg. Servicing ironically isn't that different either, in the grand scheme of things £100 or so extra servicing isn't going to matter - although indies for a Mazda are noticeably cheaper. If you go for Vredestein tyres on the BMW the tyre costs are similarly low. The Z4 is based on the 3 series, so that's where your reliability and reasonable running costs are coming from.
Good deal? I'd say it's fair as maxman said. Personally I would want a newer with less spec car that's manual, but of course that's going to increase your costs. Check out the mx5nutz forum to see what other people's experiences are with MX-5s - you've got this one for your Z4 biased info!
Oh also look into the Honda S2000. It led the reliability charts for many years, has a stonkingly fun engine and a great gear change - we're talking 9k rpm redline! It's awful as a main car, but as a second one I imagine it would be crazy fun. Make sure to get one that was regged prior to 23rd March 2006 so you don't get stung with £445 road tax.