Surah

Bismihi ta'ala 

It is very clear that no Muslim says any expression like 'Ya Rasul Allah Madad', or 'Ya Ali Madad', with the slightest of intention that they are equal to Almighty God, or that they will help independently free of any involvement from God.  

If, for argument sake, someone was to say anything like this, and believe that a Prophet, an Imam or a saint can within their own power independent from God they are performing Shirk, and this is forbidden and condemned. 

But, if we were to seek intercession, or help, or call to any of God's creation, alive or dead, who have an exceptional status in the eyes of Almighty God and they be granted this position from God, then it is not Shirk, not is it a contradiction. 

We seek forgiveness from Almighty God, but also in the Quran the Almighty says that the Prophet (s.a.w) can forgive us as well (Surah al-Nisa`, verse 64). We can also make reference to the story of Prophet Ya'qub (a.s.) and his children (Surah Yusef, 97-98). 

As for asking which one is better? Tp say Ya Allah, or Ya Ali. This kind of question is meaningless, because it entails that they are equally parallel to each other, or one replaces the other. However, it is not the case. Each expression functions within its own usage. It is like saying 'should I say Ya Rahman, or Ya Rahim'. 

Furthermore, there are many authentic traditions in both Sunni and Shia sources that validate the practice of Istighathah and Tawassul. Some Sunni scholars, like Imam al-Sabki, say it is a very good practice. In Sunni sources it also has a frequently mentioned tradition that 'remembering Ali is in itself an act of worship'. 

Therefore, there is no contradition, and Muslims throughout the history of Islam have sought help from mediums other than Allah ta'ala, without any intent of Shirk. The Almighty has appointed Prophets and Imams as mediums, and therefore we are able to get to Him through them.

Wassalam

Bismihi ta'ala

According to the main view the word 'Ameen' آمين is used to mean 'O God, answer'. So, in this case there is nothing wrong with the expression itself, even though this word does not come from the Quran, nor is it a part of any verse. 

This is something agreed upon by both Sunnis and Shi'ah. 

However, the issue is whether it is permissible to say it in a daily obligatory prayer, after reciting the Fatihah. 

Shi'a scholars say that if Ameen is said with the intention of it being a part of Salat, then the prayer will be invalid. It is a foreign word and has nothing related to the Surah, or correct dhikrs mentioned as parts of the Salat.

We are obliged to adhere to how the Prophet (s.a.w.) has taught us to pray. In the narrations there is no mentioning that the word 'Ameen' should be said after the Fatihah.

We cannot add something that does not exist in the Sunnah of the Prophet (s.a.w.), and therefore doing such a thing would nullify our Salat.  

It is a consensus of Shi'ah scholars that saying 'Ameen' in Salat, after Fatihah is an innovation and therefore would invalidate the prayer. 

Ameen is a word foreign to the prayer, and not a 'supplication'. This is contrary to the expression 'alhamdulillah rabb al-'alameen' which would be permissible to say after reciting the Fatihah, due to it being a dua and also it being mentioned to do so in authentic traditions. 

For further information on the word Ameen, see:

http://en.wikishia.net/view/Amin

And Allah knows best.