First off, good suggestions above. I'm glad to see you mention a new line on your own. I think a new, stiffer line will really help. Too limp a line will tangle easily as will an older line that's got a rough surface.
Main thing I'd add to all this is a little thing called line management. I've fished a good bit from a kayak and I'd second what Juro mentions about clearing the clutter. Also, how you prepare your line is important. Lots of lines need to be stretched after they come off a reel, particularly the older model reels with small diameters. Stretching it reduces its tendancy to lie in tight coils on the deck.
Also, if you have your line sitting in the bottom of a vessel it will probably get dirty. Make sure to clean it after every outing. Dirt causes lines to act "sticky" and tangle easier, not to mention shoot less distance.
Learning to manage line is an ongoing task, and it's not the same for every situation. If you're wading a stream or river, the coil idea Juro mentions is great. It keeps the line from being pulled downstream, which is hard to pull back for a cast.
(Wading the saltwater flats it's just the opposite: holding the line in coils will almost always result in a tangle when you cast, but letting the line drag in a big loop behind you will keep it clear and ready to cast.)
Fishing from vessels usually just means making the boat fly-line friendly. Move anything the line can catch on or, if you can't move it, drape a wet towel over it so the line won't catch on it. Or, use a clean, five-gallon bucket as a "line-tamer". Drill a few holes in the bottom for water to drain and just strip into that. If it has a tendancy to slide around on the deck, you can pain the bottom with some of that cheap rubberizer you can buy at most hardware stores - tool dip, I think it's called. Using a stripping bucket of some kind also means you can simply pick the line up and move it if you need to... a sure way of making a tangle otherwise.
Hope this helps.
PS If you're line is piling up at the end of a cast it probably means you aren't stopping the rod properly at the end of the cast. This is usually a symptom of trying to "throw" a line, rather than unroll it, as Lefty would say. Remember, the rod needs to quickly and completely stop at the end of the cast.