Contrary to what people would have you believe, the Wii U version, at least for the Raid mode, is very different from the 3DS version. It's far more refined. The 3DS version's online won't be supported much longer and it's in the online department that the first game really shined. + the 3DS version has game breaking glitches in the Raid Mode, like instance where you simply can't finish a mission because of how bad the glitches are, and they never bothered to patch those out.
Such glitches were patched out in later versionS, but the Wii U version still haD glitches of its own, like all console versions of the game? that were never patched either, at least up until the current gen re-release.
The RAID mode in the Switch version however (along with the PS4/XBONE version) will be the most complete to date, there's quite a bit of content added in there. Higher levels of customisation for the weapons and revamped stages they said (the Ghost Ship stage in particular) should bring even more depth to it.
The 3DS version is still a decent way to play it (and dirt cheap, it's frequently discounted on the eShop at 10$), but not the most ideal by a long shot, especially since they'll pull the plug on the online soon enough.