Things are never black and white... Even with the extreme conservatism of the aviation industry, if a feature only has positive effects, it would normally be there.
Some thoughts on VGs:
Their primary function is to 're-energise the boundary layer' and an therefore delay flow separation. This should e.g. delay the onset of stall on a wing at high AoA and/or increase effectiveness of control surfaces downstream of the VGs.
However, side effects include that the centre of pressure, especially at high AoA, will move compared to the design range. It can therefore have an impact on the allowable CG range. Another side effect can be that when the VG equipped wing does stall, it does so with different characteristics than without VGs, potentially with less warning and more violence. Another side effect is that, in cruise, the VGs add (potentially significantly) to the friction drag, thereby impacting cruise speed, consumption, range... The forces on the skin where the VGs are attached are small but also possibly not (in magnitude and direction) what the skin was designed to withstand.
On aileron gap filling, if you are concerned about low speed characteristics, then the gaps actually help to keep the airflow attached for longer (by allowing air to bleed from the high pressure area to the low pressure area) and should help the controls stay effective for longer.
Gliders are big on gap fillers, though, but not for low speed handling reasons. Gliders also religiously wash the dead bugs off their sleek laminar aerofoils... something power pilots tend to do less often. Some gliders also have 'negative flaps' for high speed cruise - again something which power pilots might be able to adopt but don't tend to...
Anyway, there's room for both/either/neither. The original aircraft was designed with a set of compromises to cater for a broad spectrum of users - you may well tweak it to your specific use - but most adjustments with a positive effect in one area will have a negative effect in another one.
But do keep in mind that if there is no 'approved' mod and you choose to experiment yourself, you have just become a test pilot
Morten
We all live under the same sky, but we don't all have the same horizon.