93-97 MX-6s look VERY similar in styling to '95-96 240s. It's kind of odd to say one likes the styling of one but thinks the other is ugly. They're so similar...
Anyway, since you're talking S13 verses 2nd gen MX-6, styling is your personal preference. To be honest, I prefer the looks of an S13 to the S14, and I'm driving a '96....so...
I know a LOT about MX-6 LS's seeing as I owned a '93 Probe GT for 2 years and am extremely active in the Probe community.
Mazda MX-6 LS/Ford Probe GT:2.5L V6 (KL03)164hp/155lb-ft tq for '93...94+ had 160lb-ft tq.Stock 0-60 is around 7 sec. 5-speed is obviously going to tend to get you there a little quicker than an auto.Stock 1/4 time is mid 15s 5-speed, 16ish auto.
Handling is incredible, and not "just" for a FWD. My Probe felt a lot more nose-heavy than my 240, but it was DEFINITELY just as tossable around corners and curves. Those cars handle outstandingly. PGT suspensions are slightly stiffer than the MX-6.
Interiors on the cars are also fantastic. Comfy, supportive seats, nice overall layout of controls and shifter.
Reliabilty is NOT as big of an issue as so many people in this thread have made it out to be. I put 30 thousand miles on my Probe and NEVER had a single issue with it other than general maintenence and normally occurring problems with the cars. In two years and 30k miles I replaced the water pump, valve cover gaskets, and distributor. All pretty basic stuff if you ask me, considering the issues occurred around 80. Other than that I had to buy a new battery, tires, and when I sold the car it was in need of a new passenger side rear brake caliper.
The automatic transmissions are crap, I won't deny that for a second. They start slipping and going out almost like clockwork around 90k... Granted this can be avoided if you buy a car that has had regular, proper transmission services, and the installation of an aftermarket transmission cooler makes a huge difference. At 100k my car was on presumably the original transmission fluid and I'd started to experience some issues with it around 93k or so... I added an ATF treatment and installed a transmission cooler, problems were solved entirely. I'd never have another auto again on any car with out a transmission cooler. They're amazing.
These cars are great in snow, too. I had a set of studded snow tires on my PGT in central OR where we got a good bit of snow in the winter, and MUCH preferred driving my car over my mom's AWD Subaru Forester...
Anyway, I promise if you get a 5-speed V6 Probe or MX-6 you will NOT be disappointed.

I can't describe how much I love these cars. I immensely regret selling my PGT for my 240 and will be switching back sometime next year once the 240 is paid off and I decide for sure I want to get rid of it.
http://www.mx6.com and
http://www.probetalk.com are both great sites for more info, pics, and all that good stuff.