I can't compare them because I haven't played Gates to Infinity but... from what I heard, GtI falls behind in storyline which is pretty short there.
On the other hand, you have enhanced graphics and 6th generation Pokemon.
Then again, you have limited number of starter Pokemon.
So it depends on your preferences... If you have 3DS, you may give GtI a shot and if you aren't satisfied, play EoS.