You could make the same argument about the Champions League. Arsenal and most other Premier League teams are much better than FC Copenhagen and Victoria Plzen. There is a bigger gap between West Ham and Maccabi Haifa, then there is between Mexico and Italy. Mexico beat Germany in the last World Cup and have got to the knock out stages loads of times. CONCACAF had three teams in the knock outs at 2014, Costa Rica finished top of a group that contained Italy, England and Uruguay, and only lost on penalties to Holland in the quarter finals. They have the spots they do on merit, I would say 3/4 is about a fair reflection on their strength. Europe currently has 13 (14 if hosting) which I would also say is roughly fair. Qualification should be a challenge.
I guess we'll need to agree to disagree.
To begin with - each national league should have at least 1 qualifying side - simply to maintain global interest. Thus some more talented sides will miss out perforce.
Next - and this is I suppose the biggest point of contention - I think that the top sides based on overall performance - as ranked by an appropriate system should get in no matter what.
How might this happen?
In the USA, men's basketball has a selection committee composed of very knowledgeable judges of the game. Each league has an auto-qualifier to keep interest up - but then, the remaining field is ranked top to bottom - strength of schedule, bad losses, big wins, recent performance, and so on are all factors. At the end - the committee mostly gets things right - the top sides in men's basketball get into the tourney. This sort of system fields the best sides - the ones that fans want to watch.
Italy out? No way. Portugal having to qualify - shouldn't happen. Based on strength of schedule, ranking, recent performance and so on - those teams should be in.
In short - the system I'd prefer...
1) Each conference hosts a tournament. The tournament winner is in the WC no matter what. This is important to maintain world interest in the sport.
2) The WC host nation is in no matter what - too, this is important to maintain interest.
3) Every other spot in the WC is subject to review by a panel of experts - similar to that which decides qualification for the NCAA Men's Basketball tournament. Sides are force-ranked from best to worst. The rest of the field is filled based on the force rank. This rule ensures that all the best sides are in in spite of perhaps a unfortunate losses at the worst possible time.
#3 is of course particularly difficult to implement for World Football given rampant corruption in the system.