What about chucking the whole vanilla-auto-connect-derp into the bin and make the standard rails bendable?
Every time the auto-connection has more than one possibility to connect neighbouring tracks, it does it not the way wanted by the user. In some cases possible connections even are ignored. E.g. when you try two turnouts (on the bended detour-side) with one curved piece of track, the track won't make a curve and stay straight. Or when you have two lines of tracks running next to each other and try to replace one piece of normal track with a powered track it will connect cross cutting both lines in half.

I imagine this behaviour:

• tracks are always placed in the direction the user is facing (or maybe you place the track by clicking the track you want it to connect to like logs do)
• straight tracks could be crafted into curved and vice versa.
• to achieve the old restone behaviour of vanilla tracks, curved tracks rotate clockwise when changing from unpowered to powered and rotate counter-clockwise when changing from powered to unpowered
• you can rotate the tracks by rightclicking with the crowbar

This would lead to more compact and more complex track layouts and heavily reduce the headaches.

While I see where this would be nice, either RailCraft or the other minecart related mods (e.g. Steves Carts) would need to add in comparability for this new system (IIRC)

I have no intention of supporting "compact" track layouts, there are just too many issues, this only solves a couple.