Stock Samruai (I've had 2) vs Stock Sidekick / Tracker 4-doorThe coil springs & IFS setup make the Tracker's ride MUCH MUCH MUCH smoother, and it's IFS has been a proven workhorse offroad. The A/C (works well) is a must-have here in the summer, and the added cargo space of the 4-door is welcome on longer camping trips, or if I just need to haul larger objects. I like that the truck is 'sealed'. With my ragtop, I never felt confident having anything of value in the vehicle unattended.
The power delivery of the 1.6L fuel injected engine is much more powerful, I climb hills on the freeway with ease, and I get 6 MPG MORE than I did in the samurai (the FI is way more efficient, would probably be even better in a 2 door) - at $3.50 a gallon for regular fuel, this is very important to me.
Trackers & Sidekicks can be had with fewer miles, and less money than many Samurai's out there these days. IMHO - it's an unbeatable value.
Modified v ModifiedThis is where "that depends" really comes into play. What's better? That depends - what do you want to do with your vehicle? Rock crawl, mud, snow, fire roads.....
Both vehicles can accept 29" tires without any modification, or be lifted & modified to accept 30"/31" tires (the max you want to go without costly or complex driveline upgrades) for $200-$300. These lifts are easy to do in a few hours with a friend, and basic tools. So, there's no clear winner for "ease of modification". Although I've only driven a modified Samruai, I still believe I'll be happier with my soon-to-be modified kick than I am with my modified Samruai (Still better power, gas mileage, etc).
Side Note: Search for spring spacer lift. When it comes to cheap lifts, it's a MUCH better option than a body lift. Body lifts clear space for tires, but don't get you any more ground clearance. Suspension lifts give more clearance for bigger tires AND gives you more ground clearance. Much better way to spend the $$$.
If extreme offroad is your thing, and you want to go above 31", the samurai is the better choice. It still CAN be done in the Trackick, but when going that big - there's way more options & aftermarket support (read: cheaper & easier to get help) for the sami.
FYI:My Samurai with 31" tires, RUF & Shackle reversal is a much smoother ride than the stock configuration, but nowhere near as nice as the kick. I'm lifting my Kick using the OME lift kit - it's the most expensive lift, but it's still only $700 (compared to high-end lifts for a yota or jeep, this is CHEAP). It provides for more flex, and a better ride on & off road. It's the "no compromise" lift... well... the compromise is the price
I'll have 30" or 31" tires on it by the end of the month. I'm convinced I'll be overall happier with it than the Samurai.