I have similar load times on my end on a New 3DS so I don't think it's your install
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Ditto on loading Twilight Menu. Once it's loaded launching a game is pretty fast though.
The various discussion threads around the internet talk about slow boot times from power on to Twilightmenu++ appearing, and how it is typically a symptom of the SD card either being slow or having a cluster size that Twilightmenu++ doesn't like. But nobody (that I can see) mentions games taking a long time to load FROM twilightmenu++. Except @Sami.
To be clear, you are saying games take a while to start after you select one, NOT that the menu system takes ages to show up from powering on the 3DS, correct? I don't know enough about the particular softmods for DSi vs. 3DS to know if its like comparing apples and oranges.
On 3DS you have to launch Twilight Menu like an app and then launch a game from there but i think both take a bit longer than you'd expect with first time game launches being even longer.
The first time booting a rom takes a while, but after that it's only a few seconds for me. Maybe something to do with SD card formatting/specs?
I counted it this time. First load (ever) of a game take 45 seconds or more. Subsequent loads of a game take around 20 seconds, before the first splash screen appears. I am using a modern SanDisk Ultra 64gb class 1 which was clean formatted FAT32 with 32k cluster size.
I updated twilight menu++ to the current version and there was no change.
One thing I can’t figure out is if I am using hiyaCFW or not and how this impacts speed. Been so long since I worried about the DSi I can’t remember what half of the stuff does. I have the hiya folder on my SD card, but I use twilightmenu. The ds-homebrew site’s description of hiyaCFW is confusing as fuck.
I timed my DSi; it varies a lot by game but the largest I tried (Pokemon Black 2) loaded in around 25 seconds on the first run, then loads in under 10 seconds on subsequent runs.
I recently started messing with my DSi again after a few years away from it, and you're definitely not alone in being confused by it all - I really have no idea what exactly I did to it. To refresh everything I ended up just wiping the SD card, then putting Twilightmenu on it. I can still boot into unlaunch so I must have modified the firmware / internal storage before, but I don't know if hiyaCFW is something that lives on there on the SD card.
Speaking of which, that's the same setup as my SD card, which is a 32gb Transcend. I can't seem to find my SD card reader to double check but I'm pretty sure of using 32k cluster size.
Might be worth mentioning, I have another DSi with a wildly different system boot time for no apparent reason. I set it up the exact same, but it takes 15+ seconds to boot vs the <5 of my main DSi, even when I swap SD cards. The only difference between them is that the one that takes a long time to boot is Japanese. Games take about the same time to boot so it doesn't seem directly related to your issue but who knows.
First load after a reboot takes over a minute usually. Pretty normal load times.