Yes. Fix a partition $\left<A_n\right>_{n\leq\omega}$
of $\mathbb{N}$ such that $A_n$ is infinite for each $n<\omega$, and $A_\omega$ has cardinality 3.
For $n<\omega$ let $B_\ell=\bigcup_{n\leq\ell\leq\omega}B_\ell$.
So $B_\omega=\bigcap_{n<\omega}B_n$,
for example.
Given $L\subseteq\mathbb{N}\times\mathbb{N}$, say $L$ is a \emph{full line} if it is just a line in the usual geometric sense;
that is, there are points $(a,b),(c,d)\in\mathbb{N}\times\mathbb{N}$ with $(a,b)\neq(c,d)$ and for $(x,y)\in\mathbb{N}$, we have $(x,y)\in L$
iff either
- $(x,y)\in\{(a,b),(c,d)\}$, or
- $b=d=y$, or
- $y\neq b\neq d$ and $\frac{x-a}{y-b}=\frac{c-a}{d-b}$.
For each $n<\omega$, let $\pi_n:B_n\to\mathbb{N}\times\mathbb{N}$ be a bijection such that $\pi_n``B_{n+1}$ is a full line.
Now define our family $E$ as follows:
Given $e\subseteq\mathbb{N}$,
put $e\in E$ iff either:
(a) there is $n<\omega$ such that $e\subseteq B_n$
and $\pi_n``e$ is a full line which is distinct from $\pi_n``B_{n+1}$, or
(b) $e=B_\omega$.
If clause (a) above holds,
say that $e$ is a stage $n$ line.
This family has the desired properties:
Each $e\in E$ is either infinite or has cardinality $3$,
so in particular, $\mathrm{card}(e)>2$.
If $e_1,e_2\in E$ with $e_1\neq e_2$, then $\mathrm{card}(e_1\cap e_2)\leq 1$, since in fact either:
there is $n<\omega$ such that $e_1,e_2$ are both stage $n$ lines,
in which case $\mathrm{card}(e_1\cap e_2)\leq 1$; or
there is $n<\omega$ such that $e_1$ is a stage $n$ line and $e_2\subseteq B_{n+1}$, in which case $\pi_n``e_2\subseteq\pi_n``B_{n+1}$,
and $\pi_n``B_{n+1}$ is a line distinct from $\pi_n``e_1$, so $\mathrm{card}(e_1\cap e_2)\leq 1$; or
vice versa (of last point),
so $\mathrm{card}(e_1\cap e_2)\leq 1$.
For all $a,b\in\mathbb{N}$ with $a\neq b$, there is $e\in E$ with $a,b\in e$: If $a,b\in B_\omega$ then $e=B_\omega$ witnesses this; otherwise let $m$ be largest such that $a\in B_m$, and $n$ largest such that $b\in B_n$; we may assume $m\leq n$. Now just consider the full line through $\pi_m(a)$ and $\pi_m(b)$.
There are $e_1,e_2\in E$ with $e_1\cap e_2=\emptyset$; just consider some parallel lines.
And there $e_1,e_2\in E$ with $\mathrm{card}(e_1)\neq\mathrm{card}(e_2)$, since in fact we get infinite sets in $E$ and also $B_\omega$.