From: metro Chicago, Illinois, USA
With BG, you get Antietam, Bull Run (both battles), Chickamauga, Gettysburg, and Shiloh.
With JTS Civil War Battles, you get those battles and also many other smaller, side battles within each larger campaign (not just variations on the marquee battles).
Not to mention that with JTS Civil War Battles, you get coverage of so many other campaigns and battles beyond (way beyond) the original BG roster. By the time the final installment in the series is released, the JTS CWB series will have covered every significant engagement in the American Civil War (hundreds of distinct battles, large and small; not just slight variations on the marquee battles).
With JTS CWB, you have a much, much larger pool of active PBEM opponents. With BG, you are mostly restricted to solo AI play.
If you stick with BG, you miss out on a host of game engine (and data and graphics) improvements in the JTS series of games.
And equally important: BG is a dead end, most likely never to improved (or bug fixed) again. If you stick with BG, you will miss out on all the improvements envisioned in the still alive and kicking JTS Civil War Battles series (where all updates are and will continue to be free of charge).
But, as in all things, YMMV.