Hello everyone,
Yes, in the end Mahou Shoujo Madoka Magica end its run with an ending less dark than I thought, but highly satisfying in both the way the girls are not destined anymore to become witch and in the way they did not pull a "all happy everafter". (That honestly would have been just cheesy in a situation like the one they were right up at the end)
First of all, Madoka's wish has been the most grandiose ever, actually I did not think about this possibility "deleting all witches from present, past and future before they are born".
I'll be honest, I saw the smirk from Kyubey become less evident after he heard the wish of Madoka. (Oh, poor me what I am supposed to do with these shoujos and their strange wishes? 
)
The whole concept of Cleopatra as Mahou Shoujo was a little funny, but still nothing excessively bad and they just make me crack a laugh or two on the fact that Kyubey has been creating Mahou Shoujo from the oldest time of the earth.
Sadly the only one to not revive is the "stupid" Sayaka as her wish consumed completed, but they've given enough closure to her position as well so it's all good.
Yes, because it's not like the Mahou Shoujos are now no more or relieved from their position as fighters for the world.
They now just changed enemy (the world's grief or something) and master most likely (Madoka that is something like an god now) and will just disappear when their energy is over instead of turning into witches.
Kyubey? Well, he just changed system and is still searching for more energy to delay the entropy more and more, it's not like he's defeated or anything. He is still pursuing his own and his race agenda.
I was actually worrying that he would die with some big twist at the end, but luckily he's still alive and kicking or I had to change my website design/icon/avatar. 
If I had to say one bad thing over the series is that unfortunately everyone forgot about Madoka except Homura, it has been a little heart strucking watching her mother forget about her and having only little lingering memories of her. (The ribbon now Homura is using at the end of the series)
You may be able to say now "But that's not a conclusive finale!", well no one here expected a conclusive finale as most likely it would end up with an unsatisfying ending.
It's not like I can even dream of a conclusive ending with all the stuff was running at the final moments with all the deaths and angst that was building up till the very end of the series.
Concluding, this has been quite an interesting run and I suggest this anime series to anyone looking for some unpredictable/original story with the classic dark Urobuchi's touch here and there.
If this still haven't convinced you, remember that ME, Kyubey is the main protagonist of the series! 
See you soon,
feal87
P.S. Now what we need is a animated film adaptation of this story....don't we?!