I would go for Cobalia just because the landscapes and environment looked beautiful in that planet. Plus I found it to be a more charming planet than Eudora.
Reepor (TOD) v.s. Orxon (R&C1)
Reepor.
Orxon was really hard and frustrating. 
Jasindu (ToD) vs. Ryllus (Size Matters)
Jasindu be Ryllus was annoying and Jasindu's graphics were brillant!
Nefaious Space Station(ACiT)VS Veldan(R&C)
you mean veldin…
I didnt like the Veldin in Ratchet and clank 1, but i liked the one in ratchet and clank UYA…
ah well… i'll vote for the nefarious space station. It has more windows… 
Kreeli comet(ToD) vs. Ublik passage(also ToD)
Hmmm… It's really hard for me to choose. I think I'll go with Kreeli Comet.
How about planet Viceron (ToD) vs. The Great Clock (ACiT)?
thank goodness the Great Clock is Analogue! So it be The Great Clock! (If it was digital i'd say NO!)
Veldin Vs Pokitaru
Pokitaru!
Kerwan or Igliak?
Which version of Kerwan are you referring to?
The one in the first game, Up Your Arsenal or TOD?
Well either way, I'll pick Kerwan over Iglak anyday.
How about…
Viceron (TOD) v.s. Aranos (GC)
Viceron and Aranos are actually 2 of my favorite planets‼
I think Aranos is better because when you completed Viceron, there's
nothing to do anymore.
How about this one:
Gemlik base or the Ublik pasasage?