U-212 and U-214 are answers to different problems, and therefore they are different.
U-212 is the result of a german requirement for a submarine with a non magnetic hull. This requirement has to do with the average depth of the Baltic Sea (56m). In those circumstances, the most important defence method of a submarine is just to go to the bottom and try to disappear in the sonar. Hence, the need for a non-magnetic steel hull.
Unfortunatelly, non-magnetic steel is also known in the industry as «sweet.steel.» Meaning that it is «softer» than the steel used in the U-214. Thats why a U-214 can go deeper than a U-212, although in the shallow water of the Baltic the U-212 would go un-notices while the U-214 would probably be caught by sonar.
Actually the family legacy of U-212 is not U-209, but the Thyssen project from the 1970s that resulted in the TR-1700 submarine from Argentina. The fastest Diesel-electric submarine in the world. The same basic layout with two decks is also found in the Dolphin class from Israel, although without non-magnetic steel nor AIP.
U-214s legacy is the U-209, although much changed. It is narrower and longer that U-212. It was not thought for the Baltic, but for open deep sea operation. Therefore U-214 will have no bottom of the sea limit, other than the limit imposed by the resistance of its stronger hull.
Both U-214 and U-212 can operate in shallow waters or deep waters, but U-212 has the edge on shallow water, while U-214 has the edge on deep water.
The systems can be changed and installed on either vessels, depending on the requirement of the users.
U-212 has older systems than the U-214 (which is just natural as the projects are almost 10 years apart).
Note that U-212 was never offered as an option to a navy. When it was offered to the Italian navy, there was no U-214 yet.
U-212 uses an imported combat system partially made in Norway by Kongsberg, known as MSI-90, while U-214s combat system is made in germany.by Atlas-Elektronik, being the latest version of the ISUS-90 system.
There are many differences in combat systems, but one of the most important results in U-212 being only able to fire torpedoes, while U-214 can fire both torpedoes and submarine launched sub harpoon missiles. This will change in future versions of U-212 though.
The consolidation of german naval industry ended with the competition between both models in the 1990s.
One cant just say which of them is better. The U-212 was an absolute german need for the Baltic conditions. Italy wanted an AIP submarine, and there wasnt really any real choice at the time. When a navy makes an option for a model, the most logical option is to stick to it, and thus Italy is going to get an additional two U-212.
For a navy that is going to protect shallow waters, there is no doubt about the clear superiority of U-212. In deep sea operations away from the shores, U-214 will fare better.