One of the things you want to determine first is this - do your players like this type of game? If you've got a hack and slash group, then the answer is probably no. More likely, you'll have a mix - roleplayers and rollplayers, and your hardest job won't be the plot (as you get started, a lot of times the players help you to develop the plot), it will be keeping everyone happy. Timing and pacing become quite important - excessive plot threads and conspiracy layers without revealing any of your cards can be frustrating for players. Make sure the conspiracy becomes "hot" periodically - encounters, some of which are related to the grand conspiracy, some red herrings, and also to give them enough information to keep the game from stalling out. Also, personalize the plot as much as possible - missing family members in the above Illithid plot is one way - this will get your players involved.
IMC, the party began by chasing a wayward princess into foreign lands. While there is a conspiracy going on to kill her within the church, the party was sidetracked by a much more complex conspiracy in the foreign nation. They were at first reluctant to get involved, so I had to tweak the plot to get them interested. Now they've begun to unravel the layers of the plot, but have had good battles fighting lesser elements of that plot. I think you'll also find it hard to keep a campaign "low magic." If any is present, it usually gets out of your control quickly. Just my $0.02.
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