Rather than asking the question "Is Arduino in trouble", we should ask "are other microcontrollers in trouble because of Arduino". Why do you think other manufacturers are jumping on the Arduino wago and started producing "open source Arduino clones". PICAXE has seen its days and, guess what, they now have an "open source Arduino compatible board". There are NUMEROUS Arduino clones out there. The story behind chipKitUNO32 is that Microchip asked a very reputable company, Digilent, to produce a board that is a combination of Arduino and PICmicro. Now, on the Arduino side, chipKit is easy to program; on the PIC side, however, you need MPLAB, a programmer, etc., which adds to the $26 price easily. I have a chipKit32, and numerous Arduino programs do not work on it. Arduino libraries missing on the chipKit and MAX32. So there.
The thing that the Arduino folks have to watch is quality and tech support. For example, they came out with the UNO and replace the very good FTDI chip with the ATMEGA8U2 chip. The latter is unreliable and has shown problems. I would rather have the FTDI than the 8U2, but, again, that is a matter of preference.