> One serious flaw of the proportional system
No such thing. There are lots of proportional systems, each of which have different proporties.
> like Italy and Israel both have
what you say is explicitly not true in Italy, where the biggest party/coalition is automatically given enough top-up seats to give them a majority.
> is that a small party can be the deciding vote, and have a much larger weight than it merits. For instance: center-left party gets 48% of the vote, communists (they still exist here) get 4% of the vote.
If the seats were split 48-48-4, then the party wih four seats would have as much power as the other two, since any two parties form a majority. But under PR, legislatures typically aren't split between two big parties and a small one. In Israel, for example, the largest party got 28 of 120 seats.
> Another flaw is that, in Italy at least, since it is not the voters of a given district who decide on one of several candidates, it is the political party who decides who actually gets to be on the list of people sent to parliament.
This is the same as with FPTP: the party decides on the candidate, and if it's asafe seat, that candidate is virtually certain to be elected. There are several systems of PR where voters not parties decide which of a party's candidates are elected: STV and open lists, for example.