Long throw or long stroke engines dont have any inherant weaknesses compared to short throw or oversquare motors... the only issue mainly is that because of the stroke they are slower revving than oversquare engines
For example a villiers 2F/JDL or similar engine with a 98cc long throw design will happily get to 4000rpm and maybe manage 4500rpm - its a function of the time taken for a revolution to complete. This is because the swept volume of the cylinder is in the
stroke of the cylinder not the bore
A Modern motorcycle engine of 98cc such as for example a baby ducati desmo (man, but that'd be fun on a pushbike) - can rev up to around 14000 rpm partly as a function of the oversquare design because all the swept volume is in the
bore of the cylinder, not the stroke.
There is also the fact of torsional and rotational forces. As has been said before for exactly the same weight of metal a longthrow engine will be weaker because its carrying more forces due to the longer stroke. The oversquare engine can be built lighter because there is less stress on the components - lighter components mean higher available engine speeds because you can move them faster without rotational mass becoming a problem.
The advantage of a long stroke motor is Torque. All the work in these motors is done by the torque which is a function of the stroke and the rotational forces. This is why a longstroke engine tends to be a chugging, slow revving machine but will not loose power so fast on hills and inclines
The advantage of an oversquare motor is HP. They have lower torque ratings and this is why you're little GEBE sometimes needs help up hill - because once an oversquare is out of its HP powerband the motor will start to labour
Its a case of you pays your money and takes your choice really
Jemma xx