The noun "apartheid", in my opinion is not a term that can be used on labelling any discriminatory measures.  It is a specific policy and ideology based upon racial segregation and racial superiority, this is not the case in the Israeli-Palestinian conflict and thus, in my opinion, not relevant.

There are actually quite telling parallells between a major strand of religious zionist ideology and the Boer nationalism sustaining apartheid South Africa, to wit, that the respective lands were bestowed upon their dominant ethnic groups by divine decree. As anyone with cursory knowledge of the region knows, there are also strong sentiments of racial as well as religious superiority at play in Jewish-Arab relations. These are arguably symmetric; the power distribution is not.

I recommend this book called The Other Side of Israel, by an Israeli Jew who grew up in apartheid South Africa and so has a solid basis for comparison.

Notwithstanding this, I am not too interested in the semantics of the term 'apartheid' for present purposes. I am interested in whether the discriminatory practices of Israel toward Palestinians - citizens and non-citizens - are repugnant enough to warrant, in conjunction with the illegal occupation, 'the South Africa treatment.' I agree that the policies are not as bad as South Africa's under apartheid, all things considered. But just how much better are they?

I'll grant for the sake of argument your claims about the segregation in the territories being defensible 'for security reasons' (though I disagree) and focus on discrimation against Israel's 20 percent Arab citizens. About these, you write that you "doubt it is done systematically." Mysteriously, you also claim that:

...it can be explained by two words, War and citizenship and thus are not denied the Palestinians on the grounds that they are not Jewish.  The exclusion from Israeli politics and law making makes sense for the above mentioned reasons.

I fail to see how 'citizenship' can explain discrimination against full Israeli citizens. As to war, it is true that the Arab fifth of citizens is widely mistrusted as a 'fifth column.' But I'd urge you to reconsider whether on reflection you think this justifies the following data from 2000:

Source

Israel is the only known country where the right to buy land is conditional on ethnicity. 94% of the land is either owned by the Israeli state, the Development Authority or the The Jewish National Fund (JNF), and is reserved for Jews only. Though recently challenged in the courts, this practice has overwhelming support in the ethnic majority:

Source

Given such attitudes, it's no wonder that registered Arabs face severe informal discrimination when it comes to renting on the remaining 3 percent of the land.

Much is often made of the Arab Israelis being allowed to volunteer in the military (IDF). There's some fine print here, though: muslims, with a few specific exception, are by law excluded from the military as well as from the police, the security services, and the prisons (though not as inmates).

Ingeniously, only those who have served in the military are eligible for full social benefits. Nice touch.

Additionally there are a host of special discriminatory statutes designed to curb the so-called Arab demographic bomb, ranging from a 2003 'emergency regulation' that limits the right of Arab Israelis to have their families naturalized, to lower children's allowances for non-Jews.

The above is not an exhaustive survey of the discrimination against Palestinian citizens of Israel. I submit, however, that it more than warrants the description, 'systematic.' If this is a necessary consequence of Israel being defined as a 'Jewish state' - a definition which, incidentally, any party must accept to even field candidates for Knesset - then I fear something is fundamentally flawed about the whole idea.

The world's northernmost desert wind.