both of my two LS's were a lot more reliable than my 94 mark. only problems I'v had was having to replace the plugs and coils (delaying doing that caused a cat failure that i fixed by hollowing out) a couple of times, and replacing the entire cooling system (which is kinda to be expected on most new cars with plastic cooling parts and definitely with an LS). both motors have been rock solid and my 03 does have a little rough shifting sometimes that is most likely due to the solenoid pack needing to be replaced. the 03 has over 160k on it, I probably put 40k-50k on the 00 before it was totaled out(which never had a single mechanical problem aside from the body shop messing up something that caused them to have to replace the cats on it) and my Mark was pretty reliable, but it did cost me three air bags and two compressors over the years before I swapped it out for coils. it did have to have the trans rebuilt twice and instead of having to have it rebuilt a 3rd time I got rid of it at 190k. while my cars are pretty well maintained, not of them get it taken easy on them. they have always been my hot rods and are constantly driven hard(like literally, they are never turned on and don't see at least a couple WOT pulls)
but to answer your original question, the later the year, the better they get.
personally, if I was to buy another LS, I wouldn't even consider anything older than 03, and would likely try to get an 06, just like if I were to buy another Mark (which someday I may) I probably wound buy one that wasn't a 98.
as far as between them, the Mark has a lot better options for making it a lot faster. the LS is a more refined and well balanced car that will handle a lot better than a Mark. for me, I love my LS but don't see myself ever buying another one. at this point in the game, parts are starting to become hard to find (a problem that the Mark can be effected by as well) and there is just no aftermarket support(at all...) and I am done buying automatic transmission cars for my fun car (and I would not be interested in a manual LS and have to deal with a slower V6) and I also don't think I would be wanting to drop the kind of money into a mark to do a C head blower and a Tremec swap when the current crop of mustangs are far better and a whole hell of a lot faster right off of the lot than either of the two.
so in the end I guess it would neither, the only things I am contemplating right now would be either a S550, or a different kind of LS... like either a 6 litre GTO, CTS-v or a 6.2 CTS-V or GXP. I'm sick of having to work extra hard to make a little power when there are so many other cars out there that start off with so much more and are way easier to make absurd amounts. hell the fact that few LSs or Marks could even keep up with my daily Focus just makes me not want another one even more.
