There is a simple check (mutex?) in the launcher. If you start d3 with "-launch" to directly get into the game, it will not be able to open the (locked) mpq files. See d3debug.txt (as mentioned by somebody else...) This is why it takes so long.
Code:
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[0] err=4 text=Win32 Open (32) - 'Data_D3\PC\MPQs\Cache\Win\patch-Win-9183.MPQ'
2012.04.26 19:32:02.210861000 OpenMpq - cache mpq open failed, delete failed: Data_D3\PC\MPQs\Cache\Win\patch-Win-9183.MPQ
2012.04.26 19:32:02.211067000 OpenMpq - Failed to open cache mpq: Data_D3\PC\MPQs\Cache\Win\patch-Win-9183.MPQ, 0
2012.04.26 19:32:02.212137000 OpenMpq - opening update mpq success: Data_D3\PC\MPQs\enUS\d3-update-enUS-9183.MPQ size=77148 local=77148
2012.04.26 19:32:02.212558000 OpenMpq - opening cache mpq failed: Data_D3\PC\MPQs\Cache\enUS\patch-enUS-9183.MPQ, sfilegetlasterror: 2012
2012.04.26 19:32:02.212763000 [1] err=2012 text=SFileOpenArchive - Open Failed - Data_D3\PC\MPQs\Cache\enUS\patch-enUS-9183.MPQ
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