Low-cost items always suffer more from fees, because there is often a minimum fee plus percentage depending on the payment processor (e.g. something like 50p + 5%). So if your price is close to the fixed fee, that's a large proportion. If it costs more, it's a smaller proportion. E.g. with that scheme a £2 item pays 60p fees (30%) whereas a £10 item pays £1 (10%, which is 3x less fees as a proportion than the £2 item). This is not including the fees the Scirra Store applies, which is definitely necessary since we absorb things like the cost of running the store as well as payment processor chargebacks which can cost £15 a time. We probably could not charge less without risking losing money on these things.
Not much anyone can do about this, it's just how ecommerce works. I guess you might have to put your prices up to compensate.