The only real doubts in Spanish spelling centre upon b/v and h- or its absence (haber v. a ver) and, now and again, je- versus ge- (jefe, general) — plus, in Hispanoamérica, the loss of the ce/ci v. se/si distinction. From a learning-to-read point of view, however, these features of orthographic redundancy have almost no impact.

Having taught English to Spanish youngsters, I am perfectly well aware that where two potential ways of spelling a determined sound sequence exist the chances are very high that those who do less reading will choose the wrong one. On the other hand, I was constantly struck by the puzzlement on Spanish children’s faced when asked the equivalent of “How do you spell X?” because for them that was the equivalent of asking “How do you say X” — and you’d just said it.

(*) The exception: you wrote >> There are also problems with what is written as LL. Depending on the variety of Spanish, this can be… etc. <<

That is not a problem. It is a virtue! That “what is written as LL” is realized differently in different varieties of Spanish presents no difficulty at all since it is specific to that variety of Spanish. LL is pronounced in only one way within that variety, yet all varieties can agree on using LL. That is, in fact, the Holy Grail of so many spelling systems for languages beset by strong dialect!variations.