I don’t know that it’s a problem, but I too don’t understand or perhaps have any firm belief, as some others do, that it is necessary. It is their choice, though, and if they haven’t changed it yet, they’re not likely to do it after one more complaint.
This will be a long ride, and compared to it, the first week where you go from level 1 to 2 is truly insignificant in comparison. It stops being an issue really quickly.
I suppose that’s the first important point you have to take and accept before you keep with the site.
As for the nonsensical meanings of the radicals, I suggest you actually learn them somewhere else, and then, for every Kanji, create your own mnemonic. If they have not clicked for you immediately, and you’ve already studied Kanji before, then you’re not likely to adapt to their stories, as I didn’t. You will be better off creating synonyms for every single one of them that aren’t what you’re used to, and to the ones you did not learn (there are pretty good ANKI decks for unnoficial Radicals, in the same way WK does, but with-closer-to-reality names). For this, Heisig’s method is pretty useful.
This isn’t too much work, but it is the one and only thing I have an issue with in WK. I really dislike the mnemonics.