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The heart of the issue is healthy competition (indeed, the anti-trust proceedings against Microsoft in the 90's were focused on that problem). It is very understandable Github's market-share and Microsoft's industry dominace would make this asquisition scary for those who value Github's independance.
This features list was correlated by Serphentas & bderiso.
The following people posted linked which I found helpful for compiling this document:
Github users: xkr47, austinhuang0131, awilfox, genacrys, rdococ
YCombimantor users: Yetanfou & TheAceOfHearts