the circuit well, is quite complex and it has lots of dip switches and jumpers...

Yes, it is complex and by definition it is not a true universal programmer.

Although, I am personally in favor of a professional programmmer, but at the same time I do realize that not everyone can affoard a professional programmer.

If you intend to use an ATMEL flash micro, I can suggest a relatively simple programmer.

ATMEL Flash Programmer

Final word: Go for ISP option. You wouldn't regret it