Entire volumes have been written about model year changes and standard equipment and packages so feel free to search the forum for more detailed info.
LTs can be grouped into three categories:
1999-2001 (earlier than you asked about)
2002-2004 (added integrated servo-powered brakes)
2005-present
There were several changes in 2005. The front end geometry was changed a little to help low speed handling. Opinions vary on how much it changed. Engine horsepower was increased somewhat. I rode a new 2005 right after I purchased my used '99 and it sure seemed to have more power. The electric centerstand was added. A neat gizmo although the manual stand works fine, too. The driver's seat was reshaped to help shorter riders reach the ground; this is generally considered to be a drawback but many riders customize their seats anyway and if it really bothers you, buy a used seat from a pre-05 and have it recovered. The instruments were changed and an LCD display added to the dash. The new instruments look fresh but I agree that the old speedo was easier to read. Hey, just install a GPS at your line of sight and use its digital speedo instead. The 2005 model year also saw the division of the high beam and low beam into separate modules. Probably helped a little but all the bikes benefit from an HID upgrade regardless of model year. I think a factory HID (Xenon) low beam became an option in 2005. There are aftermarket HID low beam kit available for less than $100 so don't sweat that one.
The early bikes came in three trim levels, Standard, Icon and Custom (later BMW added an Elite, later the Expedition or something, that added GPS and intercom). Each package added more standard features. By 2005 (I think) BMW dropped the packages. Later bikes could be ordered with more stuff, some accessories are dealer installed. A dealer brochure will probably help here.
Which bike is right? There are well maintained older bikes that will do 90% of what a brand new bike will do for a fraction of the cost. You have to weed through them, though, and if you guess wrong and have to replace a clutch or a final drive, you could be writing a big check. Buy it cheap enough and that's an acceptable risk.
I don't think I'd hesitate to buy a good used 2005. Some of those are getting down to reasonable levels now, and it would be mechanically pretty close to a brand new one. If you find one with some warranty left, all the better.
Intercom systems and GPS are popular options. BMW offers these, but there are aftermarket alternatives that work just as well or better, and cost much less. Lots of info on this board on those subjects as well.
Whatever you do, do NOT demo a K1200GT!