Why is ligand substitution only partial with copper(II) ions and ammonia?
Metal ion complexes have stepwise stability constants:
\begin{align}
\ce{[Cu(H2O)6]^2+ + NH3 &amp;&lt;=&gt;[$K_1$] [Cu(NH3)(H2O)5]^2+ + H2O}\\
\ce{[Cu(NH3)(H2O)5]^2+ + NH3 &amp;&lt;=&gt;[$K_2$] [Cu(NH3)2(H2O)4]^2+ + H2O}\\
\ce{[Cu(NH3)2(H2O)4]^2+ + NH3 &amp;&lt;=&gt;[$K_3$] [Cu(NH3)3(H2O)3]^2+ + H2O}\\
\ce{[Cu(NH3)3(H2O)3]^2+ + NH3 &amp;&lt;=&gt;[$K_4$] [Cu(NH3)4(H2O)2]^2+ + H2O}\\
\ce{[Cu(NH3)4(H2O)2]^2+ + NH3 &amp;&lt;=&gt;[$K_5$] [Cu(NH3)5(H2O)]^2+ + H2O}\\
\ce{[Cu(NH3)5(H2O)]^2+ + NH3 &amp;&lt;=&gt;[$K_6$] [Cu(NH3)6]^2+ + H2O}\\
\end{align}
with

\begin{align}
K_1 &amp;= \frac{{\left[ \ce{[Cu(NH3)(H2O)5]^2+} \right]}}{{\left[ \ce{[Cu(H2O)6]^2+} \right]\left[ \ce{NH3} \right]}}\\
K_2 &amp;= \frac{{\left[ \ce{[Cu(NH3)2(H2O)4]^2+} \right]}}{{\left[ \ce{[Cu(NH3)(H2O)5]^2+} \right]\left[ \ce{NH3} \right]}}\\
K_3 &amp;= \frac{{\left[ \ce{[Cu(NH3)3(H2O)3]^2+} \right]}}{{\left[ \ce{[Cu(NH3)2(H2O)4]^2+} \right]\left[ \ce{NH3} \right]}}\\
K_4 &amp;= \frac{{\left[ \ce{[Cu(NH3)4(H2O)2]^2+} \right]}}{{\left[ \ce{[Cu(NH3)3(H2O)3]^2+} \right]\left[ \ce{NH3} \right]}}\\
K_5 &amp;= \frac{{\left[ \ce{[Cu(NH3)5(H2O)]^2+} \right]}}{{\left[ \ce{[Cu(NH3)4(H2O)2]^2+} \right]\left[ \ce{NH3} \right]}}\\
K_6 &amp;= \frac{{\left[ \ce{[Cu(NH3)6]^2+} \right]}}{{\left[ \ce{[Cu(NH3)5(H2O)]^2+} \right]\left[ \ce{NH3} \right]}}\\
\end{align}

The overall stability constant is:

$$K_\text{B} = \frac{{\left[ \ce{[Cu(NH3)6]^2+} \right]}}{{\left[ \ce{[Cu(H2O)6]^2+} \right]\left[ \ce{NH3} \right]^6}} = K_1 \cdot K_2 \cdot K_3 \cdot K_4 \cdot K_5 \cdot K_6$$

(In particular, note the exponent 6.)

Furthermore, usually $K_i/K_{i+1}&gt;1$; thus, $K_1 &gt; K_2 &gt; K_3 &gt; K_4 &gt; K_5 &gt; K_6$. Consequently, it gets more and more difficult to exchange further ligands.

Therefore, the predominating complex strongly depends on the concentration of $\ce{NH3}$.
And you probably work with dilute aqueous solutions.

Simply speaking, the missing $\ce{[Cu(NH3)6]^2+}$ in aqueous solution can be attributed to the high concentration of water which is competing with ammonia for the coordination sites.