Q: How close do the buses drop off/load relative to the entrance turnstiles?
A: It depends on (a) where you're staying and (b) which park you're going to.
For a couple of examples: If you're staying at AKL and going to DAK, although your wait for the bus won't be long since the distance between the resort and the park is minimal, the AKL/AKV bus stop at DAK is pretty far away from the turnstiles.
If you're staying at POFQ and going to Epcot, not only will you not wait long for a bus--the resort and park are a 10-12 minute drive away from each other--but you'll be dropped off closer to the entrance than almost any other bus at Epcot.
Q: Lines for buses. Is that just EE and at the end of the day? Are the lines also bad throughout the day?
Lines for the buses can be awful or amazing at almost any time, although if you leave MK right after the fireworks, you are going to be in a very long line for your bus, assuming you're not staying at a monorail/boat launch resort. Lines can be nonexistent or awful at any time of the day. It depends on so many factors, it's almost impossible to know. I mean, a bus could need service mid-route, and everything could be delayed. The weather could become intolerable and everyone at whatever park could decide to leave at the same time. Just as two examples.
All that being said, when I stay at WDW, I use WDW bus transportation and it works pretty darn well most of the time.
Q: I recently learned that the skyline is at the back of EPCOT. Are there any other modes of transportation that are within the parks?
Another poster answered this--the train at MK. However, I think there still might be at least one Friendship boat inside Epcot--not that I'd recommend using it for anything other than a chance to sit down. As a mode of transportation it falls very very very short.
I hesitate to call this a "mode of transportation," but, assuming they're available--and they do sell out--one can rent an
ECV at all the parks and use at the park. It's expensive and you can't take them outside the park, but if there's a mobility issue, they are an option.