Nigh on all universities (if you're planning on going to one) accept alternative certifications to A-levels: such as a BTEC, so in regard to future-prospects it should be relatively similar. Depending on who you would be taking the A-Level/BTEC with, it may be different: can you access the sixth forms prospectus, because they should be able to inform you of what modules you would take? You could always email the admissions for your sixth form. If you know the exam board you can always look on the board's website too, to get a good idea and compare.
For anything like this, I would always personally recommend going with the option you enjoy more: you're more likely to do better, and higher grades are always preferable to having lower grades with something that may stereotypically seem to have more prestige (not that it does). Hope that helps.