Takfir

This problem will not be solved by debating over the minutiae of whether "calling someone a kafir makes someone a kafir, so Sunnis are a kafir." Of course, you can discuss it, and it could be good to discuss it historically and religiously.

However, it is an excuse being put forward for a viewpoint, and if this excuse is disproved, another one will be presented.

The problem here is mindset, in particular,
(a) lack of understanding of the Prophetic message and how the Prophet (S) reached out to all people rather than excluding people to form an elite group,

(b) arrogance and egotism - thinking that one is part of the small, elite, saved group while everyone else is wrong floats one's ego, and is one of the subtler traps of Shaytan, 

(c) a misunderstanding of the nature of Allah. Allah, as the creator of the universe, including the human being, is not so petty to kick people out of the ummah because of a handful of historical errors.

Sometimes also (d) some individiuals are benefitting from these ideologies, such as if they get followers or fans from spreading them and appealing to people's sense of clannishness.

To be fair there may also be (e) backlash against the Sunnis who call Shiis kafir and use that as an excuse for violence.

Surely we can understand that just as it is wrong for Sunnis to declare Shiis kafir, it is wrong to declare Sunnis kafir. We should treat others as we would like to be treated.

So basically these are the things that really need to addressed. A person who has humility before Allah and is not using their religious identity to bolster their own nafs or ego will not take it upon themself to decree masses of sincere people as kaafir.

Sometimes this takes time, such as years, and it won't happen in one or two sessions.

Addendum: It may depend on whether one is using the term for matters of religious law (such as marriage) or in a theological sense. It also depends on how one is using the word "agnostic".

In a theological sense, the Qur'anic term "kafir" is used for those who deny the existence of God or the blessings of God, or God's message, not for those who are genuinely uncertain. 

Insofar as an agnostic person neither affirms nor denies these things, and really doesn't know, they are somewhere in the middle (neither mu'min nor kafir). 

Some people call themselves "agnostic" because they dislike organised religion (for instance, they had a bad impression of it growing up) but they don't reject the idea of the divine. So this is not theologically the same thing as a "kafir". What it means is that they do not identify as part of a specific religious group, and also are not sure what they believe personally. Oftentimes, this type of agnostic is a genuine seeker of the truth and is in flux since they haven't found answers to their questions yet. 

However some people use "agnostic" as a loose synonym for atheism or just not caring enough to think about spiritual matters, and so this type of person could be called a kafir, meaning that they are fully engrossed in the material world and heedless of anything else.

Today there is a tendency to use "kafir" casually as a synonym for "non-Muslim". However, because we live in a sensitive era, it is good to be sensitive and thoughtful about how we use language (not the least because some people are killed on grounds of takfir). This is why when working with Qur'anic texts, I personally try to avoid translating "kafir" as "disbeliever" (or, even worse, "infidel") and instead go for a more literal translation along the lines of "deniers".

Also, it is good to remember that the Prophet and Imams were open to having dialogue with people who were not sure about their beliefs. If they were just called "kafirs" and rejected, Islam wouldn't have spread.