One of the problems is that Italy and Scotland don't have many pro contracts available, so they are limiting themselves in their depth pool by quite a lot. Of course there is the possibility of playing in foreign clubs but that doesn't usually happen until you've finished school or if you happen to based there. The development competitions in Italy and Scotland aren't that great compared to the rest of the 6 nations either so unless they're involved with the academy system of the pro sides then they are not equipped for pro rugby. Scotland has tried to rectify this by bringing in 4 national academies with BT and Italy have brought in 8 regional academy/centres so hopefully for them this will increase the ability of players coming through the system, at least the cream of the crop anyway.
When you consider that Ireland and Wales for example have 4 international class professional academies each and a decent level of domestic club competitions they have a sizeable advantage. Unless you have more pro sides, better development competitions or encourage your youngsters to join foreign academies then you have a problem with depth and competition for places.
Having your internationals all condensed in 2 sides also means you can't rotate them that often, in international clashes you could be missing over half your squad and the squad players replacing them are not of a high standard as i've touched on, Italy can't afford top quality foreign players either, relying on reject Saffas who are looking for Italian qualification.
If the Pro 12 was a competition like Super Rugby where the internationals could play in all the games then i think it would benefit them much more.
Italy's problems are severe, structural issues which not been rectified since they've joined the 6 nations.
A Rome side should be considered though, they could bring a lot more sponsorship interest and legitimacy to the Italian project. It is stupid that Benneton Treviso is involved when they are a tiny club who bring nothing to the market, and who also have no interest in developing the game in their region/province.