Both nice cars.......but both different cars too. If you want a little more "wow" factor, then GEN II, without a doubt. If you want to cruise the coastlines, or make a run to the great smokey mountains on a regular basis, then the Z06 might be more your style. But for just romping around your hometown,wherever that is, and taking a trip now and then, why not buy the Gen II Viper ? The looks of the Gen II crush the looks of the '03 Vette body, and as stated, the Vette has a few more comfort items, and will probably ride a little softer. If all you need/want is a CD player, AC, power windows, HP and handling, then the Viper is the way to go. Along with - damn, look at that Car, it's a Viper, ya don't see many of them around.
The problems you are talking about with a Viper........I don't really get where you're coming from. When you "race" a Car, run it hard, mod em out - you will see more writing about problems, and that's with any Car - but it's not the norm with a Gen II. The Viper is not a complicated mess, and I would think the Z06 is more of a "busy" set up. Maybe you're looking for reasons to not buy a Viper, but the ones you stated are not legit at all, in my opinion. There are a lot of guys on here that are into mods, and that's cool - and I understand that, because after driving any Car for awhile, most of us get used to it and you want more HP, and it's never enough. Mods mean speed, and we're all addicted to that common denominator - the speed. That's been going on forever with Car guys, no different here.
But if all you read are posts about things going wrong, and there are a lot of them, because this is a go-to place for questions, people helping each other out, then you will form that opinion. If you buy a decent Car, you won't have any of the problems you are talking about.
Plus, if I might add - I had my Viper in for an oil change. The garage I go to, is a Vette joint basically. There was a "Vette" guy (and I like em too) there, he has like 3 of em, different years, including a 1995 ZR1 - so, I thought he might have a small opinion about the Gen II Viper, just because of the body styles, in other words, he didn't just like old Vettes. My Car was sitting in the garage bay, beside his very nice, black ZR1. I complimented his Car, as I owned a ZR1 before anyway, and like them. He doesn't say a word about my Gen II, GTS Viper - that made his C4 body style, look - well, like another Vette really. I say to him, after he remains silent - what do you think about the Viper. He shrugs his shoulders and says, I'm just a GM guy and doesn't even acknowledge the Viper at all. I was like - jeeeeeeeez, you grumpy old bastard, can't even say one positive comment. This is not a bust on Vette guys in general, but to be honest, I don't think he knew what to say when my B/W '96 garage queen was sitting there. He stumbled over his words when he said the little he did say. I don't get that, I'm just a GM guy, or I'm just a Mopar guy mentality - but whatever. At least be respectful to another Car guy, especially if he compliments your Car. So, after reading all this bs I delivered - you decide on what Car to buy.
The Gen II Viper - has proven it's reliability and is built pretty simple, and basically, is a street legal race Car and looks like one too. How many have you seen in the past year on the roads ?
Still deciding............ ??