Apple didn't make the CPUs in the 13-inch MBPs that lack PEG lanes, nor did they make the PCH that only provided 12 total PCIe 3.0 lanes, Intel did.
True - that one is a complete non-issue. It's useful to know - if you need all 4 ports use the "restricted" ones for charge, connecting displays or USB. Nobody seriously expected to be able to plug 4 x 40Gbps SSD RAID arrays into an ultrabook.
The mis-reporting the GPU is news, because it solves the mystery of some MBPs apparently shipping with better-than-specified graphics, and stomps on conspiracy theories about Apple cheating by having in-store display models with better graphics. Its not really a problem, but its news.
Fake speaker grilles - practical impact: zero. Worrying, though, because its another indicator of Apple losing its way on form vs. function: Apple/Ive's best designs
have usually been functional, minimalistic and notably lacking in go-faster stripes. Not as serious as the real function-over-form issue, though: the fact that many technical decisions seem to have been forced by the Prime Directive of making the new MBPs even thinner and lighter that their predecessors.
USB-C/TB3: big problem: not enough choice of peripherals that
really do things with USB-C/TB3 that couldn't be done before to make it a big improvement. Instead, we're paying $$$ for new cables and adapters just to use the same old peripherals. If Apple had put in the work and had a less-disappointing Thunderbolt display and a decent TB3 dock available on launch day then maybe things would be different.
Price: big problem. Y'know, I can easily afford one myself, but I also have to think about what I'm going to do when work colleagues need new machines and ask what to get, when it was already an uphill struggle to convince the Powers that Be to fund a £1200 Mac over a £500 Lenovo.... now its a £1500 minimum Mac plus £100+ worth of new cables
just to use existing peripherals. Big changes in the past have usually been accompanied by big improvements in performance and functionality. Now, well, its not like you couldn't run a 4k or 5k display from the higher-specced older MBPs, and what TB3
hasn't bought is the DisplayPort 1.3 data rates needed for better 4k/5k support.
Frankly, I think the update we were all looking for, at least for the 15", was last year's 15" with the 2 TB2 ports replaced by 2 TB3/USB-C ports, refreshed processors & GPUs and everything else as-is. Its just too soon not to have at least one USB-A port.