Because Gilchrist is not as good with the bat as the others you mentioned.
Ok. In my opinion he is though. Take for example, Mahela...nothing against him, loved watching him bat - that elbow, backlift, those drives, a treat to watch. But the problem is he wasn't a good traveller. Scored havoc at home and again there is nothing wrong in that. You score as many runs as you can whenever and wherever you get the chance. But you also gotta score when you are out of your comfort zone. May well be not as much as you do at home but there can not be such a huge gap as it was in case of Mahela. Few years ago I did a little bit of research on performance in SENA countries of all Sub Continent batsmen with 5000 test runs on more. Turned out that Mahela is only batsman who has a below 40 average in those 4 countries - 31 Aus, 35 Eng, 27 S.A and 27 NZ. This ain't deserving a top 50 slot. Average of 60 at home and late 39 away, goes even worse, something like 33 if calculated outside Sub Continent.
Now look at Flower. Sample size is too low. Never played in Australia, only 1 test in SA, 2 in Eng...nothing can be drawn from there. Unbelievable in India. And very highly rated here, rightly so. In first 3 test matches in India he scored 717 runs at an average of 239!!! But those were flat pitches. Only 1 produced result, Kambli, Dravid, Sachin they all scored double centuries...in one of the tests Zimbabwe scored more than 500 runs in the second innings following on and were not even all out, 5th day finished. Dravid scored 200*, 70* and 162 in 3 innings he played in that series, averaging 432!!! I am not taking anything away, no matter how flat the wicket is, you still gotta score runs, and Andy scored plenty. Nothing wrong. I am just saying that those pitches were not very challenging. Failed in his last trip in India in 2002. Kumble and Bhajji both were in action. Zimbabwe also lost 2-0. Those 3 tests in India actually has a huge impact in his career, particularly because the sample size is so low. Don't see much elsewhere. Failed in S.A and Eng, failed in S.L. Decent in W.I, decent in N.Z, below average in Pakistan...but really, was he better than Gilchrist? Not in my book...
When I dig into Gilly I see a much better performance all around. An average of 40 in England, 45 in S.L, 65 in SA, 70 in WI, 80 in NZ! (never played in Pakistan). The only failure was that in India. I am not even sure if you can call that a failure, particularly with 2 centuries, specially that Mumbai one...one of the greatest innings on a turning track i have ever seen. 2nd one in Bangalore not bad either - against a very potent bowling line up of Zaheer, Irfan Pathan of 2004, Kumble and Harbhajan...
Only numbers here, I am not even going into the impact.
So Gilchrist better than Flower? In my book, yes. Better than Mahela? Hands down. In fact better than few others in that list as well...