Will,
I will second everything that John says, plus:
Control of the starters and bullpen for how quick of a hook you have, independent rankings for lefty/righty matchups, and setting a closer (who can be any pitcher and need not be an MLB closer). You can't quite have a true LOOGY or strict 7th inning, setup, closer scheme but you have a lot of control.
Similarly with the lineup, you choose both lefty/righty starter lineups so you can platoon and also define who will be pinch hit for when behind late in the game and the order guys will come off the bench.
I have also found the scoresheet engine to be pretty good when you have an injury in the middle of the week. More often than not, the guy I would want to sub is used and the lineup may get giggled a little bit but it doesn't do anything really stupid. Fast guys in the 1-2 spot, power hitters in 3-6, then filling out the rest. You can set something different for your lineup and it will use it (like I often go with my very best hitter in the #2 spot per what the sabermetric optimal lineup says). This is just the case where there is an injured player in the lineup you want and scoresheet has to fill the hole.
The limitation is purely MLB playing time for the week for your players (pitcher starts, IP, and PA) though you can overshoot the actuals by as much as about 10% in my experience.
You get a weekly email with detailed box scores for all the games in your league. So you get walkoff wins, outstanding defensive plays that end innings or games, rally killing double plays, etc. If one of your starters puts up a shutout during the MLB week, he will have that same kind of start (though may give up one run, but he certainly won't get blown out). Similarly, if one of your hitters has a 4 HR tear, he will almost always hit those 4 HR during your week's games, too.
In the bigger picture, the scoresheet default also has a great balance between keepers (13 MLB players) and drafting (22 more picks before the season starts, plus supplementals during the year so you end the season with 45 players total). Trading is also a lot of fun and there are no restrictive rules about that so you can really try to work things out based on your needs. My team needed to rebuild last year, so I took my best win-now assets and offered them to the league leaders in exchange for young players or prospects. In preparation for this year's draft, I traded down a bit as there weren't any great young guys to be grabbed in the first round. So instead, I can pick up two young guys to own for the year in the hopes that one of them will pan out into a keeper.
That was a bit long winded, but perhaps my enthusiasm for the system carries through. If you like the idea of a young team under construction, my P-NL507 league needs a new owner for team 6. That team owns some great prospects.
-Stefan