Electronic – Possible to have too much magnetics in Ethernet

Keep in mind that the type of ethernet that uses magnetics requires the transformer coupling in the spec. The transformers do some nice things for you, like completely decoupling common mode signals, providing significant voltage isolation, and in some cases projecting a different impedance to the electronics than what is natively on the cable.

If your whole device is floating or the connection is short with a common ground, you can present the correct impedance and voltage levels, and can ignore common mode signals, then you can in theory eliminate the transformers.

This won't work with some PHYs, since they require center tapped windings on their side. It's not uncommon for the PHY to drive the transmit pair by having the center tapped tied to power with only low side switches on each end. That effectively allows for bipolar drive with single ended switches, and is a legitimate architecture since a transformer is supposed to be there anyway. Look carefully at ethernet transformers, and you will see many offerings with center taps partly for this reason.

If you're careful, you can put just one transformer between two devices if they are physically close. Each end is still transformer coupled, so common mode rejection is there and the center tap drive trick still works. I actually did this on a small system once where both ethernet devices were contained in the same physical unit.

Things that spring to mind:

• usually, you'd model your PCB trace as transmission line that has exactly the same characteristics on the top, as on the bottom layer. As such, it doesn't make much of a difference where on the length of a trace you put the via; so instead of having these "looking like boobies" vias right next to each other, I'd just offset them enough to keep them in the middle of your trace
• R51, C5 could as well be on Top Layer
• I don't know the frequencies of your xtal or CPU, but chances are that the 125 Mbaud of Gigabit ethernet won't be much impressed :) however, if you're nervous about coupling, you might want to consider the classical star-like multiple ground-plane architecture. I don't think this'll be necessary here – Gigabit Ethernet Network PHYs aren't exactly bleeding edge in 2016, so even with some interference, they should work.
• just looking at the part of the layout I see, I'd say it might be easier to route if you just rotated the PHY by 90° – but that might break down the moment the complexity on the "processor side" of the phy comes into play.
• I think your RJ45-magnetics layout is OK; I'd probably been lazy and just routed the two diff pairs that are at the right half of the transformer "down" from the connector's pins, and the left half "up"; but that wouldn't have saved you from the one pair that crosses the other if you're supposed to access the magnetic's pads only from one side (unless you fit two traces between adjacent RJ45 pins...) . Topology is not always your friend :/

Notice: 1GE has a baudrate of 125 MBaud, i.e. even if considering the first two sidelobes, you really shouldn't be worried about frequencies above 375 MHz. With FR4 (with specific epsilon), and a lot of laziness approaching formulas, the wavelength of that frequency is roughly \$\frac15 \frac{c_0}{375\text{ MHz}}= \frac 15 \frac {3\cdot 10^8 \frac{\text m}{\text s}}{3.75 \cdot 10^8\frac1{\text s}}\approx \frac4{15}\approx 0.27\text{ m}=270\text{ mm}\$, so a 2mm trace length difference is but 2.7° phase error ... I think you'll be fine, even with a bit of unelegant routing.