Command + Tab sometimes does not switch to maximized window of app in another Space

control+F4. Cycles through the applications in that Space.
(I actually have this mapped to control+`; which I find easier to remember, being close to the cmd+`; to cycle through an application's windows.)

To change the keyboard shortcut, go to the Keyboard preferences, Keyboard Shortcuts, and Keyboard & Text Input. It's the 'Move focus to active or next window' option.

(Edit to fix the keyboard shortcuts; I didn't realise that the backtick character wasn't showing up.)

Have you considered using CMD-H to hide the application instead of minimize it? If you minimize a window, the app that owns that window is still the focused app, but if you hide an application, it will change focus to the next app in the switcher.

I can't help with the second part of your question. I assign apps to spaces so they don't clutter my spaces (even though they do sometimes - I'm looking at you, Photoshop).