Because Palpatine knew a slow, gradual takeover was easier than an immediate, hostile takeover.
Palpatine's vision wasn't one of militaristic takeover, it was one that was a lot more like the boiling frog metaphor. From Wikipedia:
The boiling frog is an anecdote describing a frog slowly being boiled alive. The premise is that if a frog is put suddenly into boiling water, it will jump out, but if the frog is put in cold water which is then brought to a boil slowly, it will not perceive the danger and will be cooked to death. The story is often used as a metaphor for the inability or unwillingness of people to react to or be aware of threats that arise gradually.
Palpatine knew that it was much more difficult to storm Coruscant and take over by force than it was to manipulate the Republic into appointing him ruler by choice.
Recall that the clone army was commissioned years before Palpatine/Dooku had convinced the Techno Union, the InterGalactic Banking Clan, etc. to join up with the Trade Federation and create the Separatist Alliance. Before that happened, all Palpatine had at his disposal was the Trade Federation's droid army and it couldn't even keep control over Naboo, let alone the Republic capitol of Coruscant.
Also recall that even with all of Palpatine's political manipulations, he still doesn't feel comfortable enough in his ability to maintain an absolute dictatorship until the Death Star is built and he decides he's finally powerful enough to dissolve the Senate.
Between the difficulty of taking the capitol, the unlikelihood of keeping the capitol, and the political fallout guaranteed to happen, it's quite obvious that manipulating the people into wanting Palpatine's control is much, much easier.
By slowly leveraging the Trade Federation conflict of Episode 1, creating the threat of war in Episode 2, and by painting the Jedi as traitors in Episode 3, he jumps to Supreme Chancellor, is granted emergency powers, and restructures the Republic... all with the cheering support of the Senate.