Consider the sphere $\{(x,y,z)\in{\mathbb{R}^3}:x^2+y^2+z^2=1\}$ and the point on the sphere $(x,y,z)=\left(\frac{1}{\sqrt{3}},\frac{1}{\sqrt{3}},\frac{1}{\sqrt{3}}\right)$. Intuitively, I thought "oh, that point lies on the "dead center" of the sphere as far the first octant is concerned", so I thought in spherical coordinates the same point should be $\left(r,\theta,\varphi)=(1,\frac{\pi}{4},\frac{\pi}{4}\right)$, but later when I was getting some inconsistent calculations I came back to this statement and when I applied the formal conversions: $$x(r,\theta,\varphi)=r\sin(\theta)\cos(\varphi)$$ $$y(r,\theta,\varphi)=r\sin(\theta)\sin(\varphi)$$ $$z(r,\theta)=r\cos(\theta)$$ I got that the point $(r,\theta,\varphi)=\left(1,\frac{\pi}{4},\frac{\pi}{4}\right)$ should actually be $(x,y,z)=\left(\frac{1}{2},\frac{1}{2},\frac{1}{\sqrt{2}}\right)$, and this has been driving me insane! Either there's some really silly arithmetic error I'm making or my geometric intuition is failing me. Which one is it?
Intuition for spherical coordinates of a highly symmetric point
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Your intuition is failing you. If you do the conversion, the point $(\frac 1{\sqrt 3},\frac 1{\sqrt 3},\frac 1{\sqrt 3})$ you first need $\cos (\theta) =\frac 1{\sqrt 3}$, which says $\theta\approx 0.955$. You do have $\phi=\frac \pi 4$
On
Your intuition is wrong. $\cos\left(\frac{\pi}4\right) = \frac{1}{\sqrt{2}}$.
The correct angle here is $\arccos\left(\frac 1{\sqrt{3}}\right)$ which does not have a closed form solution I am aware of. If $\cos(\theta) = \frac 1 {\sqrt{3}}$, then $\sin{\theta} = \sqrt{\frac{2}{3}}$. Thus $\sin(\varphi )= \frac 1{\sqrt{2}}$. Thus $\varphi = \frac \pi4$.
On
The sphere intersects the $x$, $y$, and $z$ axis at $(1, 0, 0)$, $(0, 1, 0)$, and $(0, 0, 1)$. To see if a point is in the "dead center" you can find the distance to each of these points and see if they are the same. For $(\frac{1}{2}, \frac{1}{2}, \frac{1}{\sqrt{2}})$, the distances are $1$, $1$, $\sqrt{2-\sqrt{2}}$, so it isn't in the "dead center". However, for $(\frac{1}{\sqrt{3}}, \frac{1}{\sqrt{3}}, \frac{1}{\sqrt{3}})$, the distances are all $\sqrt{2-\frac{2}{\sqrt{3}}}$.
On
Direction cosines
$$l^2 + m^2+n^2= \cos^2 \alpha+ \cos^2 \beta+ \cos^2 \gamma=1; \text {if } l=m=n, \text{then } l=m=n=\frac{1}{\sqrt 3}$$
The vector makes this angle to the coordinate axes including the $z$ axis. The parallel circle angle
$$ \theta=\pi/2 - \gamma = \pi/2 - \cos^{-1} \frac{1}{\sqrt3 }=\sin^{-1} \frac{1}{\sqrt3 }\approx 35.264^{\circ}; $$
Due to equal inclination to $x-, y-$ axes and projection on $x,y$ plane directly the azimuth (polar coordinate) angle $ \varphi= \dfrac{\pi}{4}.$
You're right of course that the point $\left( \frac{1}{\sqrt{3}}, \frac{1}{\sqrt{3}}, \frac{1}{\sqrt{3}} \right)$ is symmetric with respect to permutations of the $x,y,z$ axes, and so e.g. lies on the line of symmetry about which you can rotate $x,y,z$. But you're neglecting the fact that $(r,\theta,\varphi)$ coordinates do not transform nicely under rotations that move the $z$-axis. So you cannot reason that the angle $\theta$ must take some special value by symmetry.
You can reason this way for $\varphi$; considering the fact the point is unchanges by reflection in the plane $x = y$ guarantees that $\varphi \equiv \pi/2 - \varphi$ is either $\pi/4$ or $5\pi/4$. Clearly it's the former as it lies in the first $(x,y)$ quadrant.
But $\theta$ must be expressed differently. Note that $\theta$ is the angle made with the $z$ axis, which can equivalently be expressed in terms of the angle with the $(x,y)$ plane. Since $$\sqrt{x^2+y^2} = \sqrt{2} \times \frac{1}{\sqrt{3}} \qquad \text{ but }\qquad \sqrt{z^2} = \frac{1}{\sqrt{3}}$$ we see that in an appropriate sense you should think of your point as being "$\sqrt{2}$ times more in the $(x,y)$ plane than in the $z$ direction". This is made precise by noting $$ \theta = \arctan\frac{\sqrt{x^2+y^2}}{\sqrt{z^2}} = \arctan \sqrt{2} $$ rather than $\arctan 1 = \pi/4$. (This value of $\theta \approx 54.7^\circ$ is the so-called magic angle.)
So to correct your intuition, I think you should internalize the idea that we are in 3 dimensions; the point has equal magnitude in each direction; and $\theta$ reflects how close you are to one of three possible directions; hence, since only one third of the magnitude [squared] is concentrated in that particular direction, the angle made $\theta$ will be larger than $\pi/4$.