How serious do you want to get with your install?
OE's don't do a lot of reseach when fitting a sound system to a vehicle. It's always a compromise for them between cost, space and styling. Most speakers are in the door because they fit there and blend into the interior esily, not because they sound good.
There are some more or less rules for installing in automotive enviroments. Keep in mind, I am by no means and expert.
You want to try and equalize the length from each speaker to your ear. The kick panels are usually the best place for this. But you'd have to fabricate something and most times i run into trouble if you have a foot parking brake when building pods for this location. Also, winter becomes an issue where I live and having speakers down by my wet salty boots. If you live somewhere warm, probably not an issue. But kick panels allow closer to equal length for the speakers and angling them up can help raise the sound stage if positioned well.
You can also try aiming the speakers in the door in different directions. This would involve making some wedges or custom angled speaker rings. You'd be limited by the room available in your door enclosure too, unless you want to start cutting stuff.
Seperating the tweets and mids by more than 3 feet is usually not recommended as you run into timing issues.
That being said, mine are seperated in the 300M. The mids are in the doors and the tweets are in the sails. Sounds good to me. I took my tweets and used a 3 foot speaker wire, then moved them to multiple positions to see what the sound difference was (I used them for a couple days in each location). Sounded fine in the sails so that's what I went with. Please note, while my tweets are in the sails, they don't point straight out of the housing. They're angled by the use of a bracket so they point at my head (more or less). Took me the better part of two weeks just to get that angle right too......
Tweeters are also directional due to the frequency range they reproduce, meaning they should be pointed at your earsif possible. I've also read you can "fool" tweeters by pointing them at each other. I don't understand the physics behind it, but I guess the sound reflects or itself and gives your a sound stage.
I'd say your leg is "muffling" the sound. When you move it, the sound can travel and form as well as reflect off ambient surfaces, filling out the sound.
Unfortunately, re-aiming the speaker probably won't fix this. You most likely have to move the speaker or cut off your leg!
Check out some of the audio sound forums, there's a wealth of info out there. You just have to sift through it, use your reasoning and decide what is fact and what is fiction.
Good luck