The other weakness of the US presidential system is that when the executive and legislature are diametrically opposed (the system wasn't envisioned with parties in mind), they both still have to be able to get stuff done, so the power of the executive is expanded way beyond what's acceptable in e.g. the Westminster (parliamentary) system, and the legislature, which is technically the supreme branch (representing the will of the people directly) has to take drastic measures to overturn executive decisions.
In the Westminster system, the executive necessarily maintains the confidence of the parliament, so it can always get stuff passed through parliament while the opposition in parliament also acts as a formal mechanism to critique it. If party discipline is enforced, though, the parliament can't actually do all that much to control the executive and ends up acting as a rubber stamp (with the opposition possibly loud but impotent).
It also really depends on the local culture: if "backbench" (to use the UK terminology) government MPs aren't afraid to stand up for their values, criticize their party in government and shoot down various laws, parliament really does act independently. On the other hand, if MPs are loyal to their party above all else, there are effectively only two branches of government: the legislature-executive and the judiciary, which necessitates either a powerful (activist) judiciary or a very limiting constitution to maintain balance.
What system does your country use?