First: You don't choose $\epsilon$!
In an $\epsilon$-$\delta$ proof, you begin by taking an arbitrary $\epsilon$; you then need to show that it is possible to choose a $\delta$ that "works" for that $\epsilon$. So you are going at things exactly backwards, by first trying to work with $\delta$.
Second: You cannot "prove $\lim\limits_{x\to 2}\frac{x^2-2x+9}{x+1}$" using $\epsilon$-$\delta$ proofs. What you can try to prove is that the limit is equal to something (in this case, to $3$).
Third: $f(x)$ does not factor as $\frac{|x-2||x-3|}{|x+1|}$; what factors that way is $|f(x)-3|$.
So. Let's start from scratch, shall we?
An $\epsilon$-$\delta$ proof that $\lim\limits_{x\to 2}\frac{x^2-2x+9}{x+1}=3$ would work as follows: given some arbitrary $\epsilon\gt 0$, we must find a $\delta\gt 0$ (which may depend on $\epsilon$), with the property that if $0\lt |x-2|\lt \delta$, then we will have $\left|\frac{x^2-2x+9}{x+1} - 3\right|\lt \epsilon$.
So, let $\epsilon\gt 0$ be given. You want to make sure that
$$\left|\frac{x^2-2x+9}{x+1} - 3\right| = \left|\frac{x^2-2x+9-3x-3}{x+1}\right| = \left|\frac{x^2-5x+6}{x+1}\right| = \left|\frac{(x-3)(x-2)}{x+1}\right|$$
is small, by making sure that $|x-2|$ is small (that is, that $0\lt |x-2|\lt\delta$ for some chosen $\delta$).
Clearly, you also want to make sure that $\delta\lt \frac{|x+1|}{|x-3|}\epsilon$, because then we will have:
$$\left|\frac{x^2-x+0}{x+1}-3\right| = \frac{|x-3||x-2|}{|x+1|} \lt \delta\frac{|x-3|}{|x+1|} \lt \frac{|x+1|\epsilon}{|x-3|}\frac{|x-3|}{|x+1|} = \epsilon.$$
You can make sure that $\frac{1}{|x+1|}$ is no larger than some constant by making sure that $x$ is close enough to $2$. You can do the same thing for $|x-3|$. So then you can pick a $\delta$ that is simultaneously small enough to ensure that $\frac{1}{|x+1|}$ is smaller than some $C$, that $|x-3|$ is smaller than some $D$, and that $|x-2|$ is smaller than $CD\epsilon$. Try that.