yes, from a programmer's perspective open source solutions actually should be preferable.

i don't get whats supposed to be so great about gamestudio from a programmers perspective? lite-c is a proprietary c dialect. there often are compatibility issues if you want to use 3rd party c libraries. debugging is a pain. it's way more efficient to do gameplay code in a modern garbage collected language. for stuff where c/c++ would make sense... with gamestudio you don't have access to a lot of engine internals, so for every small thing/bug fix you could easily add/fix yourself (look into firoball's recent threads) you have to spend weeks of back and forth with jcl. for the most tricky parts of a game engine it also only uses free 3rd party libraries (physx,...).

regarding gamestudio vs. unity... in my opinion in a lot of ways they are more similar than many people think. unity has more manpower and money behind it and so it is more polished but i don't care much about the editors (most of my work gets done in blender anyway) or fancy features. what makes unity more interesting to me is the support for many platforms. windows isn't very interesting anymore as a platform.

edit:
hm... if you look at the most popular indie games of the recent years... most of them seem to use their own custom engines (minecraft, world of goo, penumbra, darwinia,...). why is that so?