If you're going to be batch converting the images anyway, I'd recommend sticking with Moonshell 2. I find it works great for manga, so long as the images are not in progressive Jpeg format. Moonshell loads many progressive Jpegs rather slowly, likely because it has to keep redrawing the image to the slow memory prior to displaying anything. A fair amount of manga found online tends to be in progressive Jpeg format, despite it not holding any real advantages over standard Jpeg. You can also scale down the image dimensions, since they are often in higher resolution than is ideal for viewing on the DS's screen. One other recommendation would be to pick up a memory expansion if you have a DS or DS Lite, as it can improve Moonshell's performance by a good margin. Also, I'd recommend using Moonshell 2.10 or higher, as some recent versions prior to that tend to freeze when loading progressive Jpegs. Here's a comparison of load times for some random pages of manga on a DS Lite with an Acekard 2 and a 4GB Toshiba Japan MicroSD, both with and without an EZFlash 3 in 1 memory expansion installed...
The first time listed is how long it takes to start drawing the image to the screen, while the second is the time until the image is fully loaded, both rounded to the nearest second. In the case of Manga, the first panels are typically viewable within a couple seconds of the image first appearing on-screen, so you don't have to wait until the image is fully loaded to begin viewing it.
421 KB, 1200 x 1687, jpeg:
+ mem: 0s, 7s
- mem: 2s, 11s
412 KB, 1210 x 1683, jpeg:
+ mem: 0s, 10s
- mem: 2s, 14s
103 KB, 1360 x 960, jpeg
+ mem: 0s, 6s
- mem: 1s, 9s
278 KB, 800 x 1137, jpeg:
+ mem: 0s, 5s
- mem: 1s, 8s
380 KB, 1100 x 1600, progressive jpeg:
+ mem: 50s, 59s
- mem: 51s, 64s
391 KB, 1130 x 1600, progressive jpeg:
+ mem: 36s, 43s
- mem: 38s, 50s
337 KB, 847 x 1200, progressive jpeg:
+ mem: 7s, 11s
- mem: 7s, 13s
+ mem cached*: 2s, 5s
- mem cached*: 3s, 8s
*In the case of the last set of progressive jpegs, Moonshell seems to cache data after viewing the first image to help decode subsequent images faster when moving from one image to the next, or when reloading the same image. This significantly improves performance, making them much more usable. The effect doesn't seem to be present on the other progressive jpegs tested here, possibly because they're larger and require more memory. The others also take significantly longer to load in general, disproportionate to their number of pixels. In general, I'd avoid viewing manga in progressive jpeg format unless you convert it to standard jpeg or something else first.
Another thing worth pointing out is that resolution seems to affect the load times more than file size, so compressing a jpeg more won't likely help it load faster, while resizing it will. The ~1200x1600 pages tested here are much larger than is necessary, and need to be viewed at 50% zoom, so resizing them to around 600x800 or 900x1200 would not only make them easier to view, but also help them load faster and save space on your MicroSD. This was just a quick test of some random pages of manga from a number of sources, but it might also be interesting to test a single image converted to various sizes and formats, to find what works best.
For batch converting images, one freeware program that works well and provides a lot of options is
Irfanview.
