Since the OP never stated that it was their intention to sell/upgrade the cards he/she grades, I would not be so quick to assume this is his/her intent.
Choosing which grading system you prefer, if you are choosing for your personal collection, is always going to be subjective, period. A good analogy for this would be like choosing which grocery store to shop in. All of them offer the same goods, it just comes down to personal preference as to which you will shop at (pricing is also a factor). Grading cards is no different; each company offers the same service, but it is up to you which to choose.
If you are in the market to sell, then PSA is going to be #1, as others have already clearly pointed out. However, if you are grading cards and plan on keeping them, then which company you choose is up to you. As others have also said before, both companies have their pros and cons. Beckett has higher grading standards, but PSA is the more popular company.
In the Pokemon side of card grading, PSA is chosen more often than Beckett.