Hi Stepho1 - hard to say without knowing which schools in particular you have narrowed it down to. More information here would allow for a better answer. However, making an assumption that both programs are accredited or have their candidacy for accreditation (this equalizes parts of the programs) some things to consider:
COST - not easy to determine from a school's website - for example - some 3+3 programs count your 4th year as undergrad, others as grad - this has implications on any undergrad scholarships you may receive; rec speaking with the financial aid offices
QOL - where will you be happy doing your undergrad years? pay attention to HOW the accelerated program runs - summers? super heavy course work with no time for anything else? does school count that 4th year double - meaning courses in the 4th year satisfy both requirements for your undergrad major and beginning of DPT degree? rec speaking with admissions or students currently enrolled in program
FLEXIBILITY - what if you change your mind and no longer want to pursue a DPT degree? what undergraduate majors are available to you?
Hope this helps you to begin a pro/con list for each program.