For my money the best reason for sidemounting is to get the needle valve (or more precisely the spray jet) and the vertical center of the fuel tank on the same level. Too many upright mount designs get the spray bar significantly higher (more than 1/4") than the highest available mounting for the tank inside the nose. When spray jet and tank center are on the same line, you get same fuel draw upright or inverted, otherwise you get variations from rich to lean. They may be minor variations, but the best flying depends on an accumulation of minor points all coming out in your favor.

The downside of side-mounting is that it throws off the lateral balance of your plane. This can be compensated for to some extent--for instance, on a one-piece profile, I will put the battery in the opposite wing at a position which balances the cylinder head/muffler on the other side. On a two-piece (removable wing) I use a flat pack and velcro it against the opposite side of the fuselage, which still leaves a little ballast necessary in the opposite wing tip, but not as much as mounting battery on fuselage center line.

The compromise I like best with typical two-stroke installations is rotating the cylinder around to somewhere like the 7 - 8 o'clock position, such as to get the muffler at BDC. This improves the aerodynamic balance by taking a lot of drag from the side of the plane to center or closer to center. Static balance is also improved, so again less ballast in opposite wingtip. (This setup works only on taildraggers, otherwise nosegear and muffler occupy the same space.) This also deposits less goo on the plane to clean up at the end of the day.

Taking this approach a step further would involve inverted mounting with rear exhaust--a well accepted pattern setup.