High grade/GPA versus finishing studies in the expected timeframe Situation:
Where I study (edit: Greece) we are generally not expected to pass all lessons on the first attempt (it is very rare actually) and often we fail multiple times before we can pass them. It is also rare to finish a school in the expected time (4 years for most schools, 5 for polytechnic) because of that, so most students finish two to three years later.

The only way to get a better grade on any lesson in the university I attend is by telling the professor to give you a failing grade, and even in other universities you can only take a few lessons again without this method, so this applies everywhere in the country.

Now, due to both a consistently bad timetable over the past 5 semesters (often ending the lessons at 9PM or even having 11 hours in one day), as well as a lot of extracurricular activity in my case (but related to the studies), it is hard to get a good grade (an equivalent GPA of 3 out of 4 is considered good in fact, not special but above average). Some malpractices by a lot of professors also play into this, but I am hoping that I am building a strong enough CV as to overcome this.

Actual Question:
Given a strong CV with a lot of related work on my own, certifications, and activity, should I try to finish in the expected 5 years of studies, but at the risk of a not-so-good GPA, or should I take more time but increase the GPA?

I am mostly interested in an academic career, for the industry I am confident that the CV I have built is more than enough to compensate for the grades.
This isn't exactly an either-or scenario. You can lengthen the time it takes to get your degree somewhat without it negatively impacting your chances of securing admission, particularly if it's a common event for students matriculating from your country. 

However, the longer you prolong your undergraduate degree program, the more you'll need to justify the extra time needed. For instance, one semester or one year is unlikely to raise red flags, but three or four years more might be much more problematic.