I'm not sure how it works in the EU as I am an American PPL student but let's ignore the small specifics and look at some general points.
Number of planes
Where I fly there are 2 flight schools; one has a fleet of about 20 planes from Grumman trainers all the way up through a Seminole. The other school has 2 planes... The obvious thing here is down time. The fact is that planes break, need routine checks and get rented by other students. A flight school with more planes (and an appropriate amount of instructors) will be able to handle these issues better. Many times I have booked a plane to find that it's in the shop and I get assigned another plane (same make and model).
Type of planes
While you cant be as picky here since sometimes geography limits you, some schools may be significantly more expensive than others. One of the nearby fields flight schools I looked at had just bought a new fleet of SR22's and were renting them at 250 USD an hour wet compared to the 100 USD an hour wet that I pay for a Piper Warrior. This can make a big difference in cost of training. Not that you are thinking this far in advance but if you do intend to one day buy a plane you may want to consider training in the type although its hard to say what kind of plane you would buy before you start flying :). If you intend on getting your instrument rating (I assume there is an EU equivalent) you will also want to make sure you are at a place that has instrument-capable planes and possibly even a precision approach system.
It also stands to reason that a place with older planes may see more down time as the planes may need more service but most old planes that I have flown are well kept. Here in the US trainer planes need to be inspected every 100 hours so they are out somewhat frequently for that already.
Number of instructors
Here in the US many instructors are doing so to get enough hours for their ATP. With that in mind instructors are subject to leave at any time if they make their hours and find a commercial job. Bigger schools will be able to reassign you to another instructor or may have better luck hiring a new instructor to fill the gap.
Type of airport
Again sometimes you can't be picky here because of geography but training at a towered airport as apposed to an uncontrolled field can help you hone in your radio work from day one. A bigger slightly more busy airport may also give you real experience with things like wake turbulence avoidance. Most larger airports also tend to have 2 runways which can help you on those windy days (depending on direction and such). They also tend to have better services like plowing, precision approaches, fuel (not all airports have gas!), pre-heats that don't take 20 minutes to show up etc. This can also be a but of a curse sometimes as larger airports are subject to traffic and you may find your self sitting on the runway waiting to take off on a nice day.
This can be a big factor for some people. Some are lucky enough to have the money to fly where its easiest for them (close to home or work) etc., while others don't have this luxury and must fly where its the cheapest. Here in the US a cheap school will still get you the same PPL that a super expensive place with a brand new SR22 will. So if your goal is simply to fly and cost is a serious factor there is nothing wrong with going with the cheaper option (which may involve driving a bit farther) as long as you factor in the potential down time of the planes or difficulty of booking them.