Let $E\to M$ be a (smooth) vector bundle and $J$ be a section of ${\rm End}(E)$ with $J^2= -{\rm Id}$. Can $J$ induce something in $$\mathscr{T}^{(r,s)}(E)=\bigsqcup_{x\in M} E^{\otimes r}\otimes (E^*)^{\otimes s},$$in general? For example, in $E^* = \mathscr{T}^{(0,1)}(E)$ one can set $(J^*\zeta)(\psi)= \zeta(J\psi)$, this $J^*$ squares to $-{\rm Id}$ and has the nice property that whenever we have a connection $\nabla$ in $E$, the identity $(\nabla_XJ^*)(\zeta)= \zeta\circ \nabla_XJ$ holds. But if I try to combine these two in the general case and set $$(J\Phi)(\zeta^1,\ldots,\zeta^r,\psi_1,\ldots,\psi_s) = \Phi(\zeta^1\circ J,\ldots ,\zeta^r\circ J,J\psi_1,\ldots, J\psi_s),$$I get the awkward sign $J^2 = (-1)^{r+s} {\rm Id}$ (which at least is consistent what with I did for $E^*$).
To summarize my question: I don't like this sign. I wanted $J^2=-{\rm Id}$ always. Is this fixable? If not, are there deeper reasons?
Let's consider the linear algebra question. Assume $E,F$ are two finite dimensional real spaces with complex structures $J_1 \colon E \rightarrow E$ and $J_2 \colon F \rightarrow F$. The space $E^{*} \otimes_{\mathbb{R}} F$ can be naturally identified with the space $ \operatorname{Hom}_{\mathbb{R}}(E,F)$ of $\mathbb{R}$-linear maps from $E$ to $F$. We have the following maps:
Note that we have $\hat{J} = \hat{J}_1 \circ \hat{J}_2 = \hat{J}_2 \circ \hat{J}_1$ so $\hat{J}$ is a product of two commuting complex structures. Also note that even if $E = F$ and $J_1 = J_2$ (which is your case), the complex structures $\hat{J}_1$ and $\hat{J}_2$ are different. Of course you can also replace $J_1,J_2$ with $-J_1,-J_2$ and get the conjugate complex structures.
In general, you can put $r+s$ different complex structures on $(E^{*})^{\otimes s} \otimes E^{\otimes r}$ which pairwise commute and induce various direct sum decompositions. Multiplying any odd number of them will give you additional complex structures.