stage 2 goes as far as possible on the standard fuel pump. stage 2+ goes as the car was far as possible with the fuel pump.
You had stage 2 with no intake before. This meant you could run aggresive settings without fuel cut. You added the intake, this increased the rate at which the car builds boost thus will result in fuel cut with a stage 2 car on the stock pump, hence they turn the boost and fueling down to compensate. The stage 2 is designed to go as far as possible without fuel cut, which is exactly what you want with a remap.
Carl is now running stage 2 software on his vRS but with a HPFP and runs much more aggressive fueling because he doesnt have to worry about fuel cut, but its more like a stage 2+ remap i guess.
similar thing with the stage 1 map and a HPFP. @ stage 1 you can easily get fuel cut, but if you add the HPFP you can run more aggressive settings and make alot more power. But thats more of a stage 1+ remap then.
As you always say though, its all about what your after in a remap. An exhaust has its benefits as it will reduces the EGT's but its expensive. The HPFP is a weak point on the car, so is a good upgrade.
As said before, next time id be tempted to go with a stage 1+ setup instead of a 2+, purely in hindsight and what i want from a car. I like performance without the noise.