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I think this something that every student asks themselves. If you concentrate on learning Spanish from one country, Spanish from another will seem different to you. Let me share my experience with you. I am from England so Spain is nearer to me than for example Mexico, however I used to travel to South America so I started to learn Spanish using a South America accent, for example pronouncing words with an ''s'' like ''vez as ves'' and ''paz as pas'' After studying for a few years I started talking with Spaniards and watching TV from Spain, the difference is huge, and it was very hard to get used to how they spoke in Spain. Now I am used to both accents and when I speak with Spaniards I pronounce words as they do, for example ''cerveza as thervetha'' For having starting to learn Spanish with an accent from South America I still find this accent the easiest for me to understand.
Also when I first started to learn Spanish I did not learn the verbs in the form of vosotros, I started years after and it is now something that I struggle with, I wish I had started to learn it from day one when I started.
A friend of who speaks Spanish very well, has trouble understanding the accents of South America, she learned Spanish whilst living in Spain and struggles with other accents.
Although it may not be possible try to learn the difference lets say how Spanish is spoken in Spain and in Mexico, concentrating on one as I did you may struggle with the other. It is only when you study both and you begin to see the differences in the other accent, that they both become clearer.
Good luck.