Guys, several technical issues pertain.
Some old 4GB cards are just SD not the new standard "SDHC" (SD 2.0 spec.) These MIGHT have some DSTT advantages as noted but are generally slower with there real, average, read and or write speeds. You should be informed that newer SDHC devices (like SDHC cameras) will lock out non-standard 4GB SD cards; for your protection. Said another way, newer SDHC devices (cams, phones) are made to not work on purpose; with regular SD that is over 2GB.
What you are noticing with the speed differences is a keen observation. The reason why is latency, access times. NDS files are huge! The newer SDHC cards transfer to and from your computer faster (the specific USB to SDHC reader matters too.) As a general rule, newer cards tend to be faster. Some 2GB SD cards are fast though too (average read/write.)
In the DS and on the DSTT you will notice VFAT16 (SD) card access time (on menu reading and save files) to be faster. VFAT16 (AKA FAT) handles these faster but not your huge NDS game loads. So latency and initial access times are different from an overall average read or write; over a longer time period.
Conclusion: It doesn't really matter. It depends on what you want to do. You will get much faster menus with VFAT16.
When buying a flash card, I notice the SD 2.0 "Class" rating (like Class 6) is of very limited value. Class 6 in just the MINIMUM write speed of 6MB/s. I would expect ANY new card to do at least that. What you'd want (most) is a fast AVERAGE read and write speed. Now, I am not a brand name kind of guy but SanDisk is the ONLY one that I have found that states (and thus commits to) a stated average sustainable read and write speed of at least 20MB/s! This is, till 40MB/s avg comes to SDHC; like it has Compact Flash. So, this is what I personally consider for a new card that I might buy. It would be price dependent. Yet, I personally can't see saving $10 and losing speed. I weight the computer transfer speed (read and write) the most; as it saves me time (every time) doing so. I advise you to get a known, matched and fast reader with your fast card or you may lose a bit of that speed (or worse.) The chip set in the reader matters.
Now, buying (MicroSD or MicroSDHC) for the DSTT specifically can be different. The real choice is between a newer 2GB (Micro)SD with a real stated read/write speed of at least 20MB/s (average not minimum) if you can find one in Micro size, and between a MicroSDHC of 4GB or better. Practically and price wise, perhaps an 8GB would hold ALL the NDS games if you didn't want to store other things on the same card. I personally do not think video played on the DS is it's best use. You will probably just want to dedicate a flash card to the DS and use others for other devices (and backups) anyway.
Category 1 - MicroSD 2GB 20MB/s (must be STATED) avg read/write points:
o VFAT16 will give faster DSTT menus and saves, You can only store about a forth of the NDS games on it (at 2GB) but that may be enough. This will also work with any SD reader for fewer compatibility issues and you will not require a reader but you'd probably want a faster one anyway. This might be a good option if your computers built in SD reader can not do the "HC" of SDHC. SIDE NOTE: I have a notebook where it's built in SD doesn't do SDHC with driver upgrades (yet) but WILL do SDHC automagically; while employing the Kubuntu OS.
o VFAT16 has an old limit to the number of files in the root directory. This is why cameras use sub directories as their standard and you should do the same with the DSTT.
Category 2 - MicroSDHC 4GB(or better) with stated 20MB/s Avg:
o VFAT32 handles larger files (NDS games) better and while it (in 4GB only) can be (still VFAT32) formatted to a similar allocation size as the VFAT16 2GB and under cards; for menu and ".sav" file speed, It may lose speed advantages conversely on loading game titles.
o Larger 4GB and 8GB MicroSDHC cards might be considered a bit cumbersome while scrolling through massive numbers of (unsorted, a DSTT lack) games. Yet you can sort the card externally; by your computer. PLEASE, do not use sorters apps that require "unmounted" lower level manipulation. This may trash Flash cards. Only use sort programs (Win or Kubuntu/Linux) that simply move files with normal and "mounted" calls. They work just as fast; all most instantly. So, do not risk it otherwise.
FLASH CARDS:
FYI: Flash cards emulate the VFAT file systems on top of their SCSI hard drive EMULATION.
The lower level file system of Flash pages differ in size than your VFAT allocation sizes and are matched/aligned to reduce slow downs and conflicts. What this means is that SOME Flash cards will get out of alignment (work erratically and undependable) if your format also CHANGES (or eliminates as with XP) the partition table. SOME Flash cards have (tiny amounts) of slack space (usually) before the actual, one, partition. This aligns THESE Flash cards with the VFAT16 (SD) OR VFAT32 (SDHC) Flash cards and this "alignment" is DIFFERENT between the VFAT32 and VFAT16 files systems. They have different page sizes. Thus on SOME cards (like 4GB AND that have that pre-partitioned slack space), If you change the files systems, you will destabilize the card. It is very difficult to "re-align" a card; If the partition table has been MOVED.
Therefore please note: Normally you would leave the format alone or if there's a problem, format in your camera. With the DSTT, it does no self formating. XP may miss "Format" your Flash card and eliminate the partition altogether (like a Floppy that has zero partition tables). XP also has had numerous errors with it's new SDHC drivers. Any "Format" utility program that also redoes the partition table; along with Formatting, may therefore destabilize your Flash. THAT is what the format scare is all about.
As noted in this forum. Panasonic has a free SD(HC) Flash formating program that has a check box that may re-align a corrupted SD/SDHC FLASH card, creating a proper partition table and VFAT.
The very special case is the (usually slower anyway) non-standard and very rare 4GB SD only (pre SDHC) Flash card. It would be formated VFAT16 in contrast. I would not change it to the standard VFAT32(or change VFAT32 to VFAT16). It likely would create the alignment issue. It may not be initially apparent. It's partition placement would be for VFAT16 and therefore not correct for the differing virtual page sizes of VFAT32. It's the real and different Flash page sizes that are fixed. VFAT paging is emulated on Flash cards.
Bottom line is, if you can get a killer deal on a 20MB/s STATED 2GB MicroSD AND you are happy with that size (and using folders) then go for it. Your menu in the DSTT will be faster and so will saves. Game loads will likely be fine. A slower SD many not run your games correctly. As you know, some Flash carts are worse with these slower MicroSD cards. So, price may be an issue in order to get a fast 2GB. You may rather pay less for a 4GB or greater SDHC with it's recommended SDHC(USB) reader.
On non-Micro SDHC, You will not likely see a huge price difference ($20 maybe) on a 4GB SDHC 20MB/s STATED (Sandisk Extream III rebated) card and with matched, fast, SDHC reader (very important. Note: The so called "SDHC" reader that comes with the DSTT doesn't work correctly!) You would have Twice (Quad with 8GB) the space, better large file management (NDS games), no root file limits, no more SDHC compatibility concerns (with a fast USB 2.0 port for the included, matched, faster, SDHC reader) and more future proofing.
If the slower menu doesn't bother you and you want more games on board, get an SDHC. If you are doing mainly smaller, homebrew files and not many large NDS games, perhaps you'd prefer a fast 2GB SD(or two).
You might say the 2GB are simpler and cheaper but not so much for the faster ones.
What complicates this is Micro cards are generally sold as slower than the full size SD cards. My above info covers both SD and MicroSD. MicroSD(HC) prices and speeds may be harder to pin down.
If you go for the cheapest. You may find a $5 deal but is it worth it to you; for every transfer to take up lots more minutes? Some close-out MicroSD cards don't runs some of the games without studdering. Is the $20 (estimated) you save, worth it?
Everyone has there own view (and cash,) Some would say get a 1GB while some would say get a 16GB. Perhaps the technical info above is helpful to you.