I've had both. Had a 2000 V6 Sport Package (Auto tranny) for 3 years and about 65k miles. Currently have a 2002 LSE V8 that I've had since brand new. Curently has 99k miles on it. The V8 is much more suited to the weight of the car, in my opinion. But..if you can locate a first gen V6 with a 5 speed stick, I say go for it. The auto tranny in these things is HORRIBLE when pressed for any performance purposes. It's durable and reliable for sure, but all the hunting between gears and pausing and hesitating (again..when pushed in performance mode) is VERY annoying. My 1999 M3 has an auto with sport and manual modes..but even in regular "E" (economy) mode, the shifting is ALWAYS precise, crisp, and right on time. In Sport mode, it's even better. Examples: In the LS, when coasting down from say...50mph to 25mph..then STOMP on the accelerator. Chances are you will get a weird freewheeling delay before the tranny decides on which gear, then actually makes that selection. In the M3, under the same circumstances, the tranny actually does an almost imperceptible DOWNSHIFT during the coasting phase, placing the car in the right gear AHEAD of time. So as soon as you press the accelerator..INSTANT action. And if you press the accelerator past a certain point and then lift up, it will remain in the downshifted gear/high rpm for several seconds prior to upshifting again...just in case you want to get down on it again. This is from a 1999 transmision (with an engineering design from 1995) with 84k miles on it.
THATS the type of quality/engineering that doesn't always show up in pricing comparisons or even magazine reviews. But once you drive it and experience it, you know its there.
Sorry to get off topic. With that said, love my LSE for my daily driver. M3 convertible is only for weekend fun.