I have both.
I bought the cartridge when the game first released and played it tons, but I did time travel and such with it.
Recently I bought the digital copy from the eShop and have been playing that more. I purchased it initially digitally so that I could carry another cartridge in the system when I traveled.
I'm really enjoying playing it properly with no time travel and starting from scratch though, and aside from not having Truffles in my town I think this is my favourite of the two now! <3
Just purchased copies of the digital version for both me and my husband this past weekend I haven't played AC since the Gamecube version, and I'm really happy to finally have a 3DS and to be playing AC again!